PROTHENA CORP PUBLIC LTD CO

Notes to the Condensed Consolidated Financial Statements

1. Organization

Description of Business

Prothena Corporation plc (“Prothena” or the “Company”) is a late-stage clinical biotechnology company with expertise in protein dysregulation with the potential to change the course of devastating neurodegenerative and rare peripheral amyloid diseases.

Fueled by its deep scientific expertise built over decades of research, the Company is advancing a pipeline of therapeutic candidates for a number of indications and novel targets for which its ability to integrate scientific insights around neurological dysfunction and the biology of misfolded proteins can be leveraged. The Company’s pipeline includes both wholly-owned and partnered programs being developed for the potential treatment of diseases including Parkinson’s disease, ATTR amyloidosis with cardiomyopathy, Alzheimer’s disease and Amyotrophic lateral sclerosis (ALS). Prothena is developing and applying its proprietary CYTOPE® technology to target a broad spectrum of intracellular targets in the brain and periphery.

The Company was formed on September 26, 2012, under the laws of Ireland and re-registered as an Irish public limited company on October 25, 2012. The Company's ordinary shares began trading on The Nasdaq Global Market under the symbol “PRTA” on December 21, 2012, and currently trade on The Nasdaq Global Select Market.

Liquidity and Business Risks

As of September 30, 2026, the Company had an accumulated deficit of $1.3 billion and cash and cash equivalents of$271.4 million.

Based on the Company's business plans, management believes that the Company’s cash and cash equivalents at September 30, 2026, are sufficient to meet its obligations for at least the next twelve months. To operate beyond such period, or if the Company elects to increase its spending on research and development programs significantly above current long-term plans or enters into potential licenses and/or other acquisitions of complementary technologies, products or companies, the Company may need additional capital. Additionally, in order to develop and obtain regulatory approval for our potential products the Company will need to raise substantial additional capital. The Company expects to continue to finance future capital needs that exceed its existing cash and cash equivalents from payments pursuant to its agreements with Roche, BMS, and Novo Nordisk, and, to the extent necessary, other collaborative agreements with corporate partners, or other arrangements, and through proceeds from public or private equity or debt financings, and loans. The Company cannot assume that such additional financings will be available on acceptable terms, if at all, and such financings may only be available on terms dilutive to its shareholders.

2. Summary of Significant Accounting Policies

Basis of Preparation and Presentation of Financial Information

These accompanying Condensed Consolidated Financial Statements have been prepared in accordance with the accounting principles generally accepted in the U.S. (“GAAP”) and with the instructions for Form 10-Q and Regulation S-X statements. Accordingly, they do not include all of the information and notes required for complete financial statements. These Condensed Consolidated Financial Statements should be read in conjunction with the Consolidated Financial Statements and Notes thereto contained in the Company’s Annual Report on Form 10-K filed with the U.S. Securities and Exchange Commission (the “SEC”) on February 27, 2026 (the “2025 Form 10-K”). These unaudited interim Condensed Consolidated Financial Statements are presented in U.S. dollars, which is the functional currency of the Company and its consolidated subsidiaries. These Condensed Consolidated Financial Statements include the accounts of the Company and its consolidated subsidiaries. All intercompany balances and transactions have been eliminated in consolidation.

Unaudited Interim Financial Information

The accompanying Condensed Consolidated Financial Statements and related disclosures are unaudited, have been prepared on the same basis as the annual consolidated financial statements and, in the opinion of management, reflect all adjustments, which include only normal recurring adjustments, necessary for a fair presentation of the results of operations for the periods presented. The year-end condensed consolidated balance sheet data was derived from audited financial statements, however certain information and footnote disclosures normally included in financial statements prepared in accordance with

GAAP have been condensed or omitted. The condensed consolidated results of operations for any interim period are not necessarily indicative of the results to be expected for the full year or for any other future year or interim period.

Use of Estimates

The preparation of the Condensed Consolidated Financial Statements in conformity with U.S. GAAP requires the Company to make judgments, estimates and assumptions that affect the reported amounts of assets, liabilities, revenues and expenses, and related disclosures. On an ongoing basis, management evaluates its estimates, including critical accounting policies or estimates relatedto revenue recognition and research and development expenses. The Company bases its estimates on historical experience and on various other market specific and other relevant assumptions that management believes to be reasonable under the circumstances, the results of which form the basis for making judgments about the carrying values of assets and liabilities that are not readily apparent from other sources. Because of the uncertainties inherent in such estimates, actual results may differ materially from these estimates.

Significant Accounting Policies

Except for the accounting policy for repurchases of ordinary shares, which was added below as a result of the Company’s February 2026 announcement of a share repurchase plan, there were no significant changes to the accounting policies during the nine months ended September 30, 2026, from the significant accounting policies described in Note 2 of the Notes to the Consolidated Financial Statements in the 2025 Form 10-K.

Repurchases of Ordinary Shares

The Company may repurchase its ordinary shares from time to time in open market transactions. All shares repurchased are immediately retired. Repurchased ordinary shares are recorded at cost and the excess of the repurchase cost over the par value of repurchased ordinary shares is charged against additional paid-in capital (“APIC”) or to accumulated deficit once APIC is reduced to zero. The par value of repurchased ordinary shares is charged against the ordinary shares par account. The Company accrues for the cost of shares repurchased based on the trade date.

Concentration of Risks and Other Risks and Uncertainties

Financial instruments that potentially subject the Company to concentration of credit risk consist of cash and cash equivalents. The Company places its cash equivalents with high credit quality financial institutions and, by policy, limits the amount of credit exposure with any one financial institution. Deposits held with banks have exceeded, and will continue to exceed, federally insured limits. The Company is exposed to credit risk in the event of a default by the financial institutions holding its cash and cash equivalents. The Company has not experienced any losses on its deposits of cash and cash equivalents and its credit risk exposure is up to the extent recorded on the Company's Consolidated Balance Sheet.

The Company’s business is primarily conducted in U.S. dollars except for its agreements with contract manufacturers for drug supplies which are primarily denominated in euros. For the nine months ended September 30, 2026, the Company recorded a gain on foreign currency exchange rate differences of approximately $231,000 and a loss of $306,000 during the nine months ended September 30, 2025. If the Company increases its business activities that require the use of foreign currencies, it may be exposed to losses if the euro and other such currencies continue to strengthen against the U.S. dollar.

The Company’s revenue during the nine months ended September 30, 2026 was primarily from revenue from the development milestone payment received from Novo Nordisk, and to a lesser extent, collaboration revenue recognized under the Company’s Collaboration Agreement with BMS, while the revenue during the nine months ended September 30, 2025 was primarily from collaboration revenue recognized under the Company’s Collaboration Agreement with BMS. During the nine months ended September 30, 2026, and 2025, the Company derived its revenue from foreign countries and none from Ireland.

As of September 30, 2026, and December 31, 2025, $2.3 million and $2.1 million, respectively, of the Company’s property and equipment, net were held in the U.S. and anominal amount were in Ireland.

The Company does not own or operate facilities for the manufacture, packaging, labeling, storage, testing or distribution of nonclinical or clinical supplies of any of its drug candidates. The Company instead contracts with and relies on third-parties to manufacture, package, label, store, test and distribute all preclinical development and clinical supplies of our drug candidates, and it plans to continue to do so for the foreseeable future. The Company also relies on third-party consultants to assist in managing these third-parties and assist with its manufacturing strategy.

Segment Information

The Company currently manages its operations as a single segment focused on the discovery and development of novel therapies to treat diseases caused by protein dysregulation. A single management team reports to the chief operating decision maker (“CODM”) who comprehensively manages the entire business. All clinical programs are included inone operating segment because the majority of the Company’s clinical programs have similar economic and other characteristics, including the nature of the clinical programs and production processes, and regulatory environment.

Consistent with the Company’s operational structure, the chief executive officer, as the CODM, manages and allocates resources at the global corporate level using consolidated, single-segment GAAP financial statement reported profit and loss and consolidated budget and forecast information for the purpose of evaluating performance, allocating resources, setting incentive targets, and planning and forecasting future periods. Managing and allocating resources at the global corporate level enables the CODM to assess both the overall level of resources available and how to best deploy these resources across functions, therapeutic areas and research and development projects in line with our overarching long-term corporate-wide strategic goals, rather than on a clinical program basis. The Company is not organized by market and is managed and operated as one business. As a single reportable segment entity, the determined measure of profit or loss is the Company’s consolidated net income (loss). Consolidated asset information for the Company’s single-segment is presented in the Company’s Consolidated Balance Sheet.

The following table sets forth significant research and development (“R&D”) expenses by program as regularly provided to the CODM (in thousands):

Recent Accounting Pronouncements

On November 4, 2024, the Financial Accounting Standards Board (“FASB”) issued Accounting Standards Update (ASU) 2024-03, Income Statement — Reporting Comprehensive Income — Expense Disaggregation Disclosures, which requires public business entities to disclose, on an annual and interim basis, disaggregated information about certain income statement line items in a tabular format in the notes to the financial statements. This guidance will be effective for the Company’s annual period ending December 31, 2027, and interim periods beginning January 1, 2028. Early adoption is permitted. Entities may apply the guidance prospectively or retrospectively. The Company is currently evaluating the impact of this new standard on its financial statement disclosures.

There have been no other recent accounting pronouncements or changes in accounting pronouncements during the nine months ended September 30, 2026 that are of significance or potential significance to the Company.

3. Fair Value Measurements

The Company measures certain financial assets and liabilities at fair value on a recurring basis, including cash equivalents. Fair value is an exit price, representing the amount that would be received to sell an asset or paid to transfer a liability in an orderly transaction between market participants. As such, fair value is a market-based measurement that should be determined based on assumptions that market participants would use in pricing an asset or a liability. A three-tier fair value hierarchy is established as a basis for considering such assumptions and for inputs used in the valuation methodologies in measuring fair value:

Level 1 — inputs are quoted prices (unadjusted) for identical assets or liabilities in active markets.

Level 2 — inputs are other than quoted prices included in Level 1 that are observable for the asset or liability, either directly or indirectly.

Level 3 — inputs are unobservable inputs that are supported by little or no market activities, which would require the Company to develop its own assumptions.

The fair value hierarchy also requires an entity to maximize the use of observable inputs and minimize the use of unobservable inputs when measuring fair value. The carrying amounts reflected in the Condensed Consolidated Balance Sheets for cash equivalents, prepaid expenses and other current assets, accounts payable and accrued liabilities, approximate their fair value due to their short-term nature.

Based on the fair value hierarchy, the Company classifies its cash equivalents within Level 1. This is because the Company values its cash equivalents using quoted market prices. The Company’s Level 1 securities consisted of $256.0 million and $275.4 million in money market funds included in cash and cash equivalents at September 30, 2026, and December 31, 2025, respectively.

4. Composition of Certain Balance Sheet Items

Prepaid Expenses and Other Current Assets

Prepaid expenses and other current assets consisted of the following (in thousands):

Property and Equipment, net

Property and equipment, net consisted of the following (in thousands):

Depreciation expense was $0.2 million and $0.6 million for the three and nine months ended September 30, 2026, compared to $0.2 million and $0.7 million for the three and nine months ended September 30, 2025, respectively.

Other Current Liabilities

Other current liabilities consisted of the following (in thousands):

5. Net Loss Per Ordinary Share

Net loss per ordinary share was determined as follows (in thousands, except per share amounts):

Potentially issuable ordinary shares were not used in computing diluted net loss per ordinary share as their effect wouldbe anti-dilutive due to the loss recorded during thethree and nine months ended September 30, 2026 and three and nine months ended September 30, 2025, and therefore diluted net loss per share is equal to basic net loss per share.

The equivalent ordinary shares not included in diluted net loss per share because their effect would be anti-dilutive are as follows (in thousands):

6. Commitments and Contingencies

Lease Commitments

As of September 30, 2026, the Company currently has two leases relating to its facilities in the United States and Dublin, Ireland.

Dublin

In June 2021, the Company entered into a lease agreement for office space in Dublin, Ireland, which commenced in August 2021 and had an initial term ofone year. In addition, the Company entered into a lease agreement for additional office space in Dublin, Ireland, which commenced in August 2023 and had an initial term ofone year. Both leases have an automatic renewal clause, pursuant to which each agreement will be extended automatically for successive periods equal to their current terms, unless each agreement is cancelled by the Company. In April 2026, the Company renewed the August 2023 lease for anotherone year term. The lease that commenced in August 2021 was not renewed and terminated pursuant to its terms on July 31, 2026.

Brisbane Facility

On October 28, 2022, the Company entered into a noncancelable operating sublease (the "Brisbane Sublease") to sublease approximately 31,157 square feet of office and laboratory space located in Brisbane, California (the “Brisbane Facility”) with Arcus Biosciences, Inc., (the "Sublandlord"). The Brisbane Sublease became effective on October 28,2022. The Brisbane Sublease provides that the Company's obligation to pay rent commenced on July 1, 2023, which is subject to abatement for the first six months following such date, with the exception of the seventh rent payment that was due upon execution of the Brisbane Sublease. The Company is obligated to make lease payments totaling approximately $14.9 million over the lease term, which expires on September 30, 2028, unless terminated earlier. The Brisbane Sublease further provides that the Company is obligated to pay the Sublandlord certain costs, including taxes and operating expenses. The Company has the option to extend the sublease by providing written notice at least nine months prior to the expiration of the sublease term. As of September 30, 2026, the Brisbane Sublease has a remaining lease term of 2.0 years.

Total operating lease cost for the Brisbane Sublease was $0.8 million and $2.4 million for the three and nine months ended September 30, 2026, respectively, and $0.8 million and $2.4 million for the three and nine months ended September 30, 2025, respectively. Total cash paid against the operating lease liability was $0.8 million and $2.4 million for the three and nine months ended September 30, 2026, respectively, and $0.8 million and $2.3 million for the three and nine months ended September 30, 2025, respectively.

In conjunction with the Brisbane Sublease, the Company obtained a standby letter of credit in the initial amount of $0.9 million, which may be drawn down by the Sublandlord in the event the Company fails to fully and faithfully perform all of its obligations under the Brisbane Sublease and to compensate the Sublandlord for all losses and damages the Sublandlord may suffer as a result of the occurrence of any default on the part of the Company not cured within the applicable cure period. As of September 30, 2026, none of the standby letter of credit amount of $0.9 million has been used.

The following table sets out a maturity analysis of payments under the Company’s operating leases, including a reconciliation to the lease liabilities recognized in the Condensed Consolidated Balance Sheets as of September 30, 2026 (in thousands):

Indemnity Obligations

The Company has entered into indemnification agreements with its current and former directors and officers and certain key employees. These agreements contain provisions that may require the Company, among other things, to indemnify such persons against certain liabilities that may arise because of their status or service and advance their expenses incurred as a result of any indemnifiable proceedings brought against them. The obligations of the Company pursuant to the indemnification agreements continue during such time as the indemnified person serves the Company and continues thereafter until such time as a claim can be brought. The maximum potential amount of future payments the Company could be required to make under these indemnification agreements is unlimited; however, the Company has a director and officer liability insurance policy that limits its exposure and enables the Company to recover a portion of any future amounts paid. As a result of its insurance policy coverage, the Company believes the estimated fair value of these indemnification agreements is minimal. Accordingly, the Company had no liabilities recorded for these agreements as of September 30, 2026, and December 31, 2025.

Other Commitments

In the normal course of business, the Company enters into various firm purchase commitments primarily related to research and development activities. As of September 30, 2026, the Company had non-cancelable purchase commitments to suppliers for $1.4 million (of which $0.4 millionis included in current liabilities), obligations under the Company’s restructuring plan of $0.6 million (of which all of it is included in current liabilities) and contractual obligations under license agreements of $35,000. The following is a summary of the Company's non-cancelable purchase commitments and contractual obligations as of September 30, 2026 (in thousands):

(1) Purchase obligations consist of non-cancelable purchase commitments to suppliers and contract research organizations.

(2) Includes cash obligations under our restructuring plan. For additional information, see Note 11, “Restructuring” to the Condensed Consolidated Financial Statements.

7. Significant Agreements

Roche License Agreement

In December 2013, the Company through its wholly owned subsidiary Prothena Biosciences Limited and Prothena Biosciences Inc entered into a License, Development, and Commercialization Agreement (the “License Agreement”) with F. Hoffmann-La Roche Ltd. and Hoffmann-La Roche Inc. (together, “Roche”) to develop and commercialize certain antibodies that target α-synuclein, including prasinezumab, which are referred to collectively as “Licensed Products.” Upon the effectiveness of the License Agreement in January 2014, the Company granted to Roche an exclusive, worldwide license to develop, make, have made, use, sell, offer to sell, import and export the Licensed Products. The Company retained certain rights to conduct development of the Licensed Products and an option to co-promote prasinezumabin the U.S. During the term of the License Agreement, the Company and Roche will work exclusively with each other to research and develop antibody products targeting alpha-synuclein (or α-synuclein) potentially including incorporation of Roche’s proprietary Brain Shuttle™ technology to potentially increase delivery of therapeutic antibodies to the brain. The License Agreement provided for Roche making an upfront payment to the Company of $30.0 million, which was received in February 2014; making a clinical milestone payment of $15.0 million upon initiation of the Phase 1 clinical trial for prasinezumab, which was received in May 2014; making a clinical milestone payment of $30.0 million upon dosing of the first patient in the Phase 2 clinical trial for prasinezumab, which was achieved in June 2017; and making a clinical milestone payment of $60.0 million upon dosing of the first patient in the global Phase 2b PADOVA study for prasinezumab, which was achieved in May 2021.

For prasinezumab, Roche is obligated to pay:

•up to $290.0 million upon the achievement of development, regulatory, and various first commercial sales milestones;

•up to $155.0 million upon achievement of U.S. commercial sales milestones;

•up to $175.0 million upon achievement of ex-U.S. commercial sales milestones; and

•tiered, high single-digit to high double-digit royalties in the teens based on U.S. and ex-U.S. annual net sales, subject to certain adjustments, with respect to the applicable Licensed Product.

Roche bore 100% of the cost of conducting the research collaboration under the License Agreement during the research term, which expired December 31, 2017. In May 2021, the Company exercised its rights under the terms of License Agreement to receive potential U.S. commercial sales milestone and royalties, in lieu of a U.S. profit and loss share for prasinezumab in Parkinson’s disease. Thus, in the U.S., through May 28, 2021, the parties shared all development costs, all of which were allocated 70% to Roche and 30% to the Company, for prasinezumab in the Parkinson’s disease indication. If the Company opts in to participate in co-development and co-funding for any other Licensed Products and/or indications, the parties will share all development and commercialization costs, as well as profits, all of which will be allocated 70% to Roche and 30% to the Company.

The Company has an option under the License Agreement to co-promote prasinezumab in the U.S. in the Parkinson’s disease indication. If the Company exercises such option, it may also elect to co-promote additional Licensed Products in the U.S. approved for Parkinson’s disease. Outside the U.S., Roche will have responsibility for developing and commercializing the Licensed Products. Roche bears all costs that are specifically related to obtaining or maintaining regulatory approval outside the U.S. and will pay the Company a variable royalty based on annual net sales of the Licensed Products outside the U.S.

The term of the License Agreement will continue on a Licensed Product-by-Licensed Product and country-by-country basis until the expiration of all Roche Royalty Terms with respect to all Licensed Products. The License Agreement may also be terminated (i) by Roche at will after the first anniversary of the effective date of the License Agreement, either in its entirety or on a Licensed Product-by-Licensed Product basis, upon 90 days’ prior written notice to the Company prior to first commercial sale and 180 days’ prior written notice to Prothena after first commercial sale, (ii) by either party, either in its entirety or on a Licensed Product-by-Licensed Product or region-by-region basis, upon written notice in connection with a material breach uncured 90 days after initial written notice, and (iii) by either party, in its entirety, upon insolvency of the other party. The License Agreement may be terminated by either party on a patent-by-patent and country-by-country basis if the other party challenges a given patent in a given country. The Company’s rights to co-develop Licensed Products under the License Agreement will terminate if the Company commences certain studies for certain types of competitive products. The Company’s rights to co-promote Licensed Products under the License Agreement will terminate if the Company commences a Phase 3 study for such competitive products.

The License Agreement cannot be assigned by either party without the prior written consent of the other party, except to an affiliate of such party or in the event of a merger or acquisition of such party, subject to certain conditions. The License Agreement also includes customary provisions regarding, among other things, confidentiality, intellectual property ownership, patent prosecution, enforcement and defense, representations and warranties, indemnification, insurance, and arbitration and dispute resolution.

Performance Obligations

As of September 30, 2026, and December 31, 2025, there wereno remaining performance obligations under the License Agreement since the obligations related to research and development activities were only for the Phase 1 clinical trial and the remaining obligations were delivered or performed.

Milestone Accounting

Under the License Agreement, the Company is eligible to receive certain milestone payments upon the achievement of development, regulatory and various first commercial sales milestones. Milestone payments are evaluated under ASC Topic 606. Factors considered in this determination included scientific and regulatory risk that must be overcome to achieve each milestone, the level of effort and investment required to achieve the milestone, and the monetary value attributed to the milestone. Accordingly, the Company estimates payments in the transaction price based on the most likely approach, which considers the single most likely amount in a range of possible amounts related to the achievement of these milestones. Additionally, milestone payments are included in the transaction price only when the Company can conclude it is probable that a significant revenue reversal will not occur in future periods when the milestone is achieved.

The Company excludes the milestone payments and royalties in the initial transaction price calculation because such payments are considered to be variable considerations with constraint. Such milestone payments and royalties will be recognized as revenue once the Company can conclude it is probable that a significant revenue reversal will not occur in future periods.

The clinical and regulatory milestones under the License Agreement after the point at which the Company could opt out are considered to be variable considerations with constraint due to the fact that active participation in the development activities that generate the milestones is not required under the License Agreement, and the Company can opt out of these activities. There are no refunds or claw-back provisions and the milestones are uncertain of occurrence even after the Company has opted out. Based on this determination, these milestones will be recognized when the Company can conclude it is probable that a significant revenue reversal will not occur in future periods.

Roche did not achieve any milestones under the License Agreement during thethree and nine months ended September 30, 2026 and 2025, respectively.

Collaboration Agreement with Bristol Myers Squibb

On March 20, 2018, the Company, through its wholly owned subsidiary Prothena Biosciences Limited (“PBL”), entered into a Master Collaboration Agreement (the “Collaboration Agreement”) with Celgene Switzerland LLC (“Celgene”), a subsidiary of Celgene Corporation (which was acquired by Bristol Myers Squibb (“BMS”) in November 2019), pursuant to which Prothena granted to Celgene a right to elect in its sole discretion to exclusively license rights both in the U.S. (the “US

Rights”) and on a global basis (the “Global Rights”), with respect to the Company’s programs to develop and commercialize antibodies targeting tau, TDP-43 and an undisclosed target (the “Collaboration Targets”).

The Collaboration Agreement provided for Celgene making an upfront payment to the Company of $100.0 million, plus future potential license exercise payments and regulatory and commercial milestones for each program under the Collaboration Agreement, as well as royalties on net sales of any resulting marketed products. In connection with the Collaboration Agreement, the Company and Celgene entered into a Share Subscription Agreement on March 20, 2018, under which Celgene subscribed to 1,174,536 of the Company’s ordinary shares for a price of $42.57 per share, for a total of approximately $50.0 million.

Term and Termination

The term of the Collaboration Agreement expired on May 24, 2024.

Performance Obligations

At inception of the Collaboration Agreement, there were a total of six options, including US Rights and Global Rights to acquire an exclusive license to develop, manufacture and commercialize antibodies targeting the applicable Collaboration Target in the U.S. (each, a “US License”) or globally (each, a “Global License”), respectively, and rights to request certain development services (following exercise of the US Rights and Global Rights, respectively) for each of the three programs. None of which were remaining as of May 24, 2024. The deferred revenue balance as of September 30, 2026 wasnil.

US License Agreement for the Tau/Moponetug Collaboration Target

BMS exercised its US Rights for the tau/moponetug (formerly BMS-986446/PRX005) Collaboration Target and on July 30, 2021, PBL entered into a U.S. License Agreement granting BMS an exclusive license to develop, manufacture and commercialize tau Collaboration Products in the United States targeting tau (the “Tau US License Agreement”). The Company received an associated option exercise fee of $80.0 million.

Global License Agreement for the Tau/Moponetug Collaboration Target

Subsequently, BMS exercised its Global Rights for the tau/moponetug Collaboration Target and on July 5, 2023, PBL entered into a Global License Agreement granting BMS an exclusive license to develop, manufacture and commercialize tau Collaboration Products globally for any and all uses or purposes with respect to any human or animal disease, disorder or condition (the “Tau Global License Agreement”). The Tau Global License Agreement supersedes and replaces the Tau US License Agreement in its entirety. The Company received an associated option exercise fee of $55.0 million in August 2023 and it is eligible to receive regulatory and sales milestones up to $562.5 million upon achievement of certain events, including regulatory approval of a tau Collaboration Product, and on BMS achieving certain annual, worldwide net sales thresholds. The Company also is eligible to receive tiered royalties on net sales of tau Collaboration Products, ranging from high single digit to high teen percentages, on a weighted average basis depending on the achievement of certain net sales thresholds. BMS will continue to pay royalties on a Collaboration Product-by-Collaboration Product and country-by-country basis, until the latest of (i) expiration of certain patents covering the Collaboration Product in such country of sale, (ii) expiration of any regulatory exclusivity for the Collaboration Product in such country of sale, and (iii) an agreed period of time after the first commercial sale of the Collaboration Product in such country of sale (the “Royalty Term”). The term of the Tau Global License Agreement will continue on a Licensed Product-by-Licensed Product and country-by-country basis until the expiration of all Royalty Terms with respect to all Licensed Products.

Global License Agreement for the undisclosed/PRX019 Collaboration Target

On May 24, 2024, PBL entered into a Global License Agreement granting BMS an exclusive license to develop, manufacture and commercialize Collaboration Products targeting an undisclosed target (including PRX019) globally for any and all uses or purposes with respect to any human or animal disease, disorder or condition (the “PRX019 Global License Agreement”). The Company received an associated option exercise fee of$80.0 million in June 2024 and is eligible to receive further development and regulatory milestones of up to$242.5 million upon achievement of certain development and regulatory milestones, including regulatory approval, of a Collaboration Product, and up to$375.0 million upon BMS achieving certain annual, worldwide net sales thresholds. The Company also is eligible to receive tiered royalties on annual, worldwide net sales of Collaboration Products, ranging from high single digit to high teen percentages, on a weighted average basis depending on the achievement of certain net sales thresholds. Such milestones and royalty payments (i) could be reduced in the case where

BMS is successful in developing a modified version of PRX019 that achieves certain specified improved metrics, and (ii) are subject to certain reductions as specified in the PRX019 Global License Agreement. BMS will continue to pay royalties on a Collaboration Product-by-Collaboration Product and country-by-country basis until the end of the Royalty Term. The term of the PRX019 Global License Agreement will continue on a Licensed Product-by-Licensed Product and country-by-country basis until the expiration of all Royalty Terms with respect to all Licensed Products. See Note 12, “Subsequent Events” for information regarding the termination of the PRX019 Global License Agreement.

The PRX019 Global License Agreement included the following distinct performance obligations: (1) the delivery of the Global License for the undisclosed Collaboration Target (“PRX019 Global License Obligation”); and (2) the Company’s obligation to run a Phase 1 clinical trial for PRX019. Pursuant to the terms of the PRX019 Global License Agreement, BMS may elect to assume responsibility for completing such Phase 1 clinical trial (at its cost). Revenue allocated to the PRX019 Global License Obligation was recognized when the Company satisfied its obligation at a point in time, while the revenue allocated to the PRX019 Phase 1 Clinical Trial Obligation is recognized over time using an input-based model.

Transaction Price

Upon entering into the Tau Global License Agreement, the Company granted BMS a Global License for the tau/moponetug Collaboration Target, which transferred control of such underlying Global License to BMS. Following execution of the Tau Global License Agreement, BMS paid the Company a $55.0 million option exercise fee. Under the continuation of the original contract method, the Company computed the relative sales price after the Company transferred control of the Global License for tau/moponetug. The Company used the original allocated consideration for the Global Right for tau/moponetug of $17.9 million (computed at the inception of the contract) plus the $55.0 million option exercise fee to arrive at the total transaction price of approximately $72.9 million. Given that the Company’s distinct performance obligation under the Tau Global License Agreement was limited to the Tau Global License Obligation no further allocation was required.

Upon entering into the PRX019 Global License Agreement, the Company granted BMS a Global License for the undisclosed/PRX019 Collaboration Target, which transferred control of such underlying Global License to BMS. Following execution of the PRX019 Global License Agreement, BMS paid the Company an $80.0 million option exercise fee. As the original contract contemplated a US and Global payment for $80.0 million and $55.0 million, respectively, and a new payment structure and only one license was agreed to, accordingly, the payment was accounted for under modification accounting. The Company concluded that the modification would be accounted for on a prospective basis as a termination of the existing contract and creation of a new contract. The Company computed the relative sales price for the identified remaining performance obligations consisting of the Global License for PRX019 and the PRX019 Phase 1 Clinical Trial Obligation. The transaction price consisted of the original allocated consideration for the US Right for PRX019 of $24.9 million, and original allocated consideration for the Global Right for PRX019 of $17.4 million (both computed at the inception of the Collaboration Agreement) plus the $80.0 million option exercise fee to arrive at the total transaction price of approximately $122.4 million. This total transaction price was allocated using the relative sales price method between the PRX019 Global License Obligation and the PRX019 Phase 1 Clinical Trial Obligation.

The best estimate of selling price for the Global License for PRX019 was based on a discounted cash flow model. The key assumptions used in the discounted cash flow model used to determine the best estimate of selling price for the license included the market opportunity for commercialization of PRX019, the probability of successfully developing/commercializing PRX019, the remaining development costs for PRX019, and the estimated time to commercialization of PRX019 using a discount rate of 13%. Based on the relative selling price method, the amount that the Company allocated to the performance obligations was as follows: $106.3 million to the license to be recognized concurrent with the delivery of the license; and $16.1 million as development services for the Phase 1 clinical trial to be recognized based on input-based model over the service period.

Significant Payment Terms

The upfront payment of $100.0 million was received in April 2018, while all option fees and milestone payments are due within 30 days after the achievement of the relevant milestone by BMS or receipt by BMS of an invoice for such an amount from the Company.

Revenue Recognition

For the three and nine months ended September 30, 2026, collaboration revenue from BMS was $0.6 million and $2.7 million respectively, and $2.4 million and $9.6 million for thethree and nine months ended September 30, 2025, respectively. Collaboration revenue for thethree and nine months ended September 30, 2026 and 2025 was related to the Company’s partial performance of its PRX019 Phase 1 Clinical Trial Obligation.

As of September 30, 2026, the aggregate amount of the transaction price allocated to the performance obligations that are unsatisfied wasnil. The Company hadnil andnil accounts receivable from BMS at September 30, 2026, and December 31, 2025, respectively.

Deferred Revenue

The deferred revenue balance at the beginning of the quarter was $0.6 million. During the three months ended September 30, 2026, $0.6 million of deferred revenue was recognized as collaboration revenue related to the PRX019 Phase 1 Clinical Trial Obligation performed. As of September 30, 2026, the total deferred revenue balance wasnil.

Milestone and Royalties Accounting

Under the Tau Global License Agreement, the Company is eligible to receive milestone payments of up to $187.5 million upon the achievement of certain specified regulatory milestones and milestone payments of up $375.0 million upon the achievement of certain specified commercial sale milestones. Under the PRX019 Global License Agreement, the Company is eligible to receive milestone payments of up to $242.5 million upon the achievement of certain specified development and regulatory milestones and milestone payments of up $375.0 million upon the achievement of certain specified commercial sale milestones. See Note 12, “Subsequent Events” for information regarding the termination of the PRX019 Global License Agreement.

Milestone payments are evaluated under ASC Topic 606. Factors considered in this determination included scientific and regulatory risk that must be overcome to achieve each milestone, the level of effort and investment required to achieve the milestone, and the monetary value attributed to the milestone. Accordingly, the Company estimates payments in the transaction price based on the most likely approach, which considers the single most likely amount in a range of possible amounts related to the achievement of these milestones. Additionally, milestone payments are included in the transaction price only when the Company can conclude it is probable that a significant revenue reversal will not occur in future periods.

BMS did not achieve any milestones under either the Tau Global License Agreement or the PRX019 Global License Agreement during thethree and nine months ended September 30, 2026 and 2025 respectively.

Novo Nordisk Share Purchase Agreement

On July 8, 2021, the Company together with its wholly owned subsidiary, PBL, entered into a definitive share purchase agreement with Novo Nordisk A/S and Novo Nordisk Region Europe A/S (each an unrelated party). Under the terms of such agreement, Novo Nordisk acquired PBL’s wholly-owned subsidiary, Neotope Neuroscience Limited (“NNL”) and gained full worldwide rights to the intellectual property and related rights to the Company’s ATTR amyloidosis business and pipeline. Upon consummation of the transaction, NNL ceased to be a related party of PBL. The aggregate purchase price consisted of an upfront payment of $60.0 million in cash, subject to customary purchase price adjustments.

Should Novo Nordisk achieve certain stages of development or commercialization for products or product candidates containing coramitug (formerly PRX004)or a derivative thereof in ATTR amyloidosis, PBL is entitled to receive certain milestone payments based on specified development and commercial milestones. The development and commercialization milestone payments will be discounted if the milestone events are achieved with respect to other indications. Should Novo Nordisk achieve specified thresholds of worldwide, annual net sales of the milestone products, regardless of indication, PBL will also be entitled to receive specified one-time net sales milestone payments. All milestone payments attributable to an achieved milestone will be paid to PBL, subject to Novo Nordisk’s offset right for indemnity claims or unpaid amounts in respect of any purchase price adjustment.

Contingent Consideration/Milestone Accounting

As of September 30, 2026, the Company is eligible to receive additional sales milestone payments from Novo Nordisk totaling up to $1.08 billion upon achievement of certain specified commercial sales milestones under the share purchase agreement. During the nine months ended September 30, 2026, the Company received a $50.0 million development milestone payment related to the continued advancement of coramitug in the Phase 3 CLEOPATTRA clinical trial. Novo Nordisk did not achieve any milestones under the share purchase agreement during the three and nine months ended September 30, 2025. Such milestone payment is recognized as revenue at a point in time when the Company can conclude it is probable that a significant revenue reversal will not occur in future periods. There are no remaining performance obligations under the share purchase agreement. The Company hadno accounts receivable from Novo Nordisk as of September 30, 2026, and December 31, 2025, respectively.

8. Shareholders' Equity

Ordinary Shares

As of September 30, 2026, the Company had 100,000,000 ordinary shares authorized for issuance with a par value of $0.01 per ordinary share and 51,341,036 ordinary shares issued and outstanding. Each ordinary share is entitled toone vote and, on a pro rata basis, to dividends when declared and the remaining assets of the Company in the event of a winding up. As of September 30, 2026,16,393,435 ordinary shares are reserved for issuance pursuant to outstanding and future equity awards under the Company’s equity incentive plans.

Euro Deferred Shares

As of September 30, 2026, the Company had 10,000 Euro Deferred Shares authorized for issuance with a nominal value of €22 per share. No Euro Deferred Shares are outstanding at September 30, 2026. The rights and restrictions attaching to the Euro Deferred Shares rank pari passu with the ordinary shares and are treated as a single class in all respects.

Share Repurchase Plan

On February 27, 2026, the Company announced a share repurchase plan under which the Company may repurchase up to $100.0 million of the Company's outstanding ordinary shares. The Company may repurchase the shares from time to time in open market transactions, which may be structured to occur in accordance with the requirements of Rule 10b-18 of the Securities Exchange Act of 1934, as amended. It may also enter into Rule 10b5-1 plans to facilitate repurchases. The share repurchase plan will expire on December 31, 2026, may be suspended or discontinued at any time, and does not obligate the Company to acquire any amount of ordinary shares. For the three and nine months ended September 30, 2026, the Company repurchased 501,492 shares and 2,745,380 shares, respectively, at an average repurchase price of approximately $8.61 and $9.69 per share, respectively, for an aggregate amount of approximately $4.3 million and $26.6 million, respectively, excluding commissions.

9. Share-Based Compensation

Equity Incentive Plans

The Company’s equity incentive plans, the 2018 Long Term Incentive Plan, as amended (the “2018 LTIP”),2020 Employment Inducement Incentive Plan, as amended (the “2020 EIIP”), and previously, the Amended and Restated 2012 Long Term Incentive Plan (the “2012 LTIP”), reserve ordinary shares for the issuance of stock options, stock appreciation rights, restricted shares, RSUs, performance bonus awards, performance share units awards, dividend equivalents and other share or cash-based awards to eligible individuals. Options granted under each of the 2018 LTIP, 2020 EIIP, and 2012 LTIP expire no later thanten years from the date of grant.

As of September 30, 2026, the number of ordinary shares authorized under the 2018 LTIP was 18,641,433. Upon adoption of the 2018 LTIP, no new awards are permitted under the 2012 LTIP.

As of September 30, 2026, the number of ordinary shares authorized under the 2020 EIIP was 1,485,000 and 696,163 ordinary shares remained available for future awards under the 2020 EIIP. The Company’s Board of Directors has adopted a series of amendments to increase the ordinary shares available for issuance under the 2020 EIIP and it reserves the right to both amend the 2020 EIIP to increase the number of ordinary shares available and make additional awards to key new hires.

The Company’s option awards generally vest over four years, while RSU awards generally vest over eithertwo orthree years. As of September 30, 2026,4,542,176 ordinary shares remained available for grant under the Company’s equity incentive plans.

Share-based Compensation Expense

Share-based compensation expense recorded in these Condensed Consolidated Financial Statements was based on awards granted under the 2012 LTIP, the 2018 LTIP, and the 2020 EIIP. The estimated forfeiture rate as of September 30, 2026 was 8%. Changes in our estimates and assumptions relating to forfeitures may cause us to realize changes in stock-based compensation expense in the future.

The amount of unearned share-based compensation related to unvested stock options at September 30, 2026, is $28.6 million. The weighted-average period over which this unearned share-based compensation is expected to be recognized is 2.78 years.

The following table summarizes share-based compensation expense for the periods presented (in thousands):

(1)Restructuring costs for the nine months ended September 30, 2026 and 2025 includes $1.7 million and $2.1 million of share-based compensation expense related to the contractual acceleration of vesting of certain option and restricted stock unit award agreements.

The Company recognizedno tax benefits for the three and nine months ended September 30, 2026 and 2025 due to the Company’s full valuation allowance on its deferred tax assets.

The fair value of the options granted to employees and non-employee directors during the three and nine months ended September 30, 2026 and nine months ended September 30, 2025 was estimated as of the grant date using the Black-Scholes option-pricing model using the key assumptions listed in the following table. There were no stock options granted during the three months ended September 30, 2025, thus no key assumptions are shown in the table below.

The fair value of employee stock options is amortized on a straight-line basis over the requisite service period for each award. Each of the inputs discussed above is subjective and generally requires management judgment to determine.

The following table summarizes the Company’s stock option activity during the nine months ended September 30, 2026:

The following table summarizes the activity and related information for RSUs during the nine months ended September 30, 2026:

As of September 30, 2026, total compensation cost not yet recognized related to unvested RSUs was $6.8 million, which is expected to be recognized over a weighted-average period of 2.21 years. RSUs settle into ordinary shares upon vesting.

Cash Settled RSU Awards

In July 2025, the Company granted RSU awards to certain employees under the 2018 LTIP. Such awards have a three-year vesting schedule, with the first vesting date in July 2026, with subsequent vesting dates in July 2027 and July 2028, and settle in ordinary shares of the Company upon vesting. Prior to the first vesting date, the Company’s Compensation Committee (and Board of Directors, in the case of the Company’s CEO) approved an amendment to modify certain RSU Award Agreements such that the holders were offered the choice to receive settlement in the form of cash rather than in the form of ordinary shares of the Company. In July 2026, the Company offered and certain RSU award holders accepted the option to receive cash settlement for all or a portion of the RSU awards that vested pursuant to their terms as of July 28, 2026. On July 28, 2026,369,600 vested RSUs were settled in cash for an aggregate amount of $3.2 million.

This cash settlement modification meets the criteria for short-term inducement under ASC 718 and the Company determined the modification date as the date the RSU award holders accepted the offer to receive settlement of the RSU awards in the form of cash. The Company calculated the fair value of the RSU awards immediately before and after the respective dates that the individual award holders accepted the offer to cash settle the RSU awards, resulting in.an incremental share-based compensation expense of $1.0 million. The cash settlement feature represents a cash-funded obligation and as a result, the modified RSU awards no longer qualify for equity classification under ASC 718. Accordingly, on the modification date, the Company reclassified the awards from equity to liabilities and remeasured the liabilities at fair value with changes recorded in the Statement of Operations until settlement.

Net-share Settled RSU Awards

In July 2025, the Company granted RSU awards to certain employees under the 2018 LTIP. Such awards have a three-year vesting schedule, with the first vesting date in July 2026, with subsequent vesting dates in July 2027 and July 2028, and settle in ordinary shares of the Company upon vesting. Prior to the first vesting date, the Company’s Compensation Committee (and Board of Directors, in the case of the Company’s CEO) approved an amendment to the RSU Award Agreements with respect to the portion of the RSUs that were scheduled to vest in July 2026 whereby the Company would withhold shares (rather than sell shares in the market) to satisfy the tax withholding obligations. In July 2026, upon vesting of 147,840 shares of these RSUs, the Company withheld 53,701 ordinary shares with a fair market value of $8.56 for an aggregate tax withholding amount of $0.5 million and the remaining 94,139 ordinary shares were issued to employees.

10. Income Taxes

The major taxing jurisdictions for the Company are Ireland and the U.S. The Company recorded an income tax expense of$2.0 thousand and$5.0 thousand for the three and nine months ended September 30, 2026, as compared to an income tax benefit of $0.4 million and an income tax expense of $43.3 million for the three and nine months ended September 30, 2025, respectively. The provision for income taxes differs from the statutory tax rate of 12.5% applicable to Ireland primarily due to Irish exempt income, Irish and U.S. net operating losses, for which a tax provision benefit is not recognized due to the full valuation allowance against deferred tax assets, and U.S. income taxed at different rates.

The income tax provision reflects the estimate of the effective tax rate expected to be applicable for the full year and the Company re-evaluates this estimate each quarter based on its forecasted tax expense for the full year. Jurisdictions with a projected loss for the year where no tax benefit can be recognized are excluded from the estimated annual effective tax rate.

Deferred income taxes reflect the net tax effect of temporary differences between the carrying amount of assets and liabilities for financial reporting purposes and the amounts used for income tax purposes. The Company's deferred tax assets (“DTAs”) are composed primarily of its Irish subsidiaries' net operating loss carryforwards, federal net operating loss carryforwards and California net operating loss carryforwards available to reduce future taxable income of the Company's U.S. subsidiaries, federal and California tax credit carryforwards, capitalized R&D, share-based compensation, and other temporary differences.

As of each reporting date, the Company considers new evidence that could affect the future realization of DTAs by jurisdiction. Valuation allowances are established if there is uncertainty that a portion or all of the DTAs will not be realized. The ultimate realization of a DTA is dependent upon the generation of future taxable income of the proper character in appropriate jurisdictions to obtain benefit from the reversal of temporary differences and net operating loss carryforwards.

Management performs an assessment of its DTAs each period. Based upon the weight of available evidence, management continues to believe that it is not more likely than not the Company will realize the benefits of its DTAs. Accordingly, the Company had a full valuation allowance against its federal, state and Irish DTAs as of September 30, 2026.

No provision for income tax has been recognized on undistributed earnings of the Company’s U.S. subsidiaries as the Company considers the U.S. earnings to be indefinitely reinvested.

11. Restructuring

In June 2025, the Company commenced a restructuring plan following the Company’s May 23, 2025 announcement of its decision to discontinue further development of birtamimab. Restructuring charges primarily consisted of employee termination benefits in connection with the reduction in force announced in June 2025 and contract termination costs primarily associated with exit fees relating to third-party manufacturers that were contracted for commercial supplies of birtamimab. Employee termination benefits include severance costs, employee-related benefits, and non-cash share-based compensation expense related to the acceleration of the vesting of certain stock options and RSUs. Charges and other costs related to the restructuring plan are presented as restructuring costs in the Condensed Consolidated Statements of Operations.

The Company recorded a net increase in the restructuring liability ofapproximately $0.2 million and a net reduction of approximately$12.7 million for thethree and nine months ended September 30, 2026, respectively. The Company may also incur additional costs not currently contemplated due to events that may occur as a result of, or that are associated with, the restructuring plan.

The following table summarizes the restructuring liability and utilization by cost type associated with the restructuring activities during thethree and nine months ended September 30, 2026(in thousands):

(1)Restructuring charges for contract termination costs for the nine months ended September 30, 2026 include a reduction in contract termination costs associated with one or more third-party vendors.

(2)Restructuring charges for termination benefits for the nine months ended September 30, 2026 include a $1.7 million share-based compensation expense related to the contractual acceleration of vesting of certain option and restricted stock unit award agreements.

The total amount expected to be incurred at inception in connection with the restructuring plan was $32.6 million. The cumulative amount incurred to date as of September 30, 2026 was $28.7 million. The restructuring liability is included in current liabilities on the Condensed Consolidated Balance Sheets as of September 30, 2026.

12. Subsequent Events

In October 2026, following an internal strategic review, Bristol Myers Squibb informed Prothena that it decided not to advance PRX019 further in the clinic.

Pursuant to the PRX019 Global License Agreement, in addition to the upfront payment, the Company was eligible to receive further development, regulatory, and sales milestones of up to $617.5 million. The Company was also eligible to receive tiered royalties on annual, worldwide net sales of Licensed Products. In connection with termination of the PRX019 Global License Agreement, Bristol Myers Squibb will not owe any of the foregoing to the Company.