Neurogene Inc.

Item 1. Condensed Consolidated Financial Statements

Condensed Consolidated Balance Sheets

(In Thousands, Except Share Information)

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Condensed Consolidated Statements of Operations

(In Thousands, Except Share and Per Share Amounts)

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Condensed Consolidated Statement of Stockholders’ Equity

(In Thousands, Except Share Information)

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Condensed Consolidated Statements of Cash Flows

(In Thousands)

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NEUROGENE INC.

NOTES TO CONDENSED CONSOLIDATED FINANCIAL STATEMENTS (UNAUDITED)

1. Organization and Description of Business

Neurogene Inc. (formerly known as Neoleukin Therapeutics, Inc. (“Neoleukin”)) (the “Company” or “Neurogene”) is a clinical-stage biotechnology company that is a result of the reverse merger. The operating entity of Neurogene Inc. is the wholly owned subsidiary incorporated in the state of Nevada and also named Neurogene Inc. (“Neurogene OpCo”). Neurogene OpCo was incorporated as a limited liability company in Delaware on January 26, 2018 and converted into a Delaware corporation on July 3, 2018, and then merged with a wholly owned subsidiary of the parent company and re-domiciled to Nevada on December 18, 2023 after completing a reverse merger with Neoleukin Therapeutics, Inc. (the “Closing”), in accordance with the terms of the Agreement and Plan of Merger, dated as of July 17, 2023 (the “Merger Agreement”). Both Neurogene and Neurogene OpCo have a principal place of business in New York, NY. Neurogene was formed to harness the power of gene therapy, combined with its EXACTTM transgene regulation technology, to turn today’s complex, devastating neurological diseases into treatable conditions. The Company’s first clinical-stage program to utilize the EXACT technology is NGN-401, which has completed dosing in a Phase 1/2 clinical trial for the treatment of Rett syndrome. The Company has also completed dosing in its registrational trial of NGN-401 to treat Rett syndrome. The trial, known as the Embolden TM study, is a single‑arm, baseline‑controlled, open‑label study evaluating NGN‑401 in females with Rett syndrome and has been designed to support a potential Biologics License Application ("BLA") submission. Since beginning operations, the Company has devoted substantially all its resources to conducting research and development activities and undertaking preclinical studies, establishing the Company’s manufacturing facility, conducting clinical trials and the manufacturing of product used in the Company’s clinical trials and preclinical studies, business planning, developing and maintaining its intellectual property portfolio, hiring personnel, raising capital, and providing general and administrative support for these activities.

2. Risks and Uncertainties

The Company is subject to risks common to companies in the biotechnology industry, including, but not limited to, successful development of technology, obtaining additional funding, protection of proprietary technology, compliance with government regulations, risks of failure of preclinical studies, clinical studies and clinical trials, risks related to personnel changes and other disruptions at federal agencies, including the U.S. Food and Drug Administration ("FDA"), and uncertainty related to those disruptions, the need to obtain marketing approval for its drug candidates and its consumer products, fluctuations in operating results, economic pressure impacting therapeutic pricing and reimbursement, dependence on key personnel, risks associated with changes in technologies, development by competitors of technological innovations and the ability to transition from pilot scale manufacturing to large scale production.

Liquidity and Financial Condition

Since its inception, the Company has funded its operations primarily with outside capital (e.g., proceeds from the sale of preferred stock, common stock, and pre-funded warrants) and has incurred significant recurring losses, including net losses of $94.4 million and $65.6 million for the nine months ended September 30, 2026 and 2025, respectively. In addition, the Company used cash in operations of $79.0 million and $59.7 million for the nine months ended September 30, 2026 and 2025, respectively, and had an accumulated deficit of $447.1 million as of September 30, 2026. Management expects to incur substantial and increasing losses in future periods as the Company advances its products through its clinical and regulatory process and will rely on outside capital to fund its operations for the foreseeable future. The Company has not generated positive cash flows from operations, and there are no assurances that the Company will be successful in obtaining an adequate level of financing for the development and commercialization of its product candidates.

As of September 30, 2026, the Company had cash, cash equivalents and short-term investments of approximately $359.7 million. In July 2026, the Company completed a public offering of common stock and pre-funded warrants, generating aggregate net proceeds of approximately $134.9 million after deducting underwriters’ discount and commissions and offering expenses. During the nine months ended September 30, 2026, the Company sold 889,054 shares of its common stock under the Sales Agreement, and received net proceeds of $31.8 million after deducting commissions and other offering expenses. For more information on the Sales Agreement, see Note 11, Stockholders’ Equity—At-The-Market Offering of Shares. The Company expects its available cash, cash equivalents and short-term investments as of the issuance dateof these financial statements will be sufficient to fund its obligations as they become due for at least one year beyond the issuance date of these financial statements.

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In the event the Company is unable to secure additional outside capital, management will be required to seek other alternatives which may include, among others, a delay or termination of clinical trials or the development of its product candidates, temporary or permanent curtailment of the Company’s operations, a sale of assets, or other alternatives with strategic or financial partners.

The accompanying condensed consolidated financial statements do not include any adjustments that might result from the outcome of these uncertainties. Accordingly, the condensed consolidated financial statements have been prepared on a basis that assumes the Company will continue as a going concern and which contemplates the realization of assets and satisfaction of liabilities and commitments in the ordinary course of business.

3. Summary of Significant Accounting Policies

Basis of Presentation

The accompanying unaudited condensed consolidated financial statements have been prepared in accordance with accounting principles generally accepted in the United States of America (“U.S. GAAP”) and pursuant to the rules and regulations of the United States Securities and Exchange Commission (“SEC”) for interim financial information. Accordingly, these financial statements do not include all of the information and footnotes required by U.S. GAAP for complete financial statements and should be read in conjunction with the audited consolidated financial statements and accompanying notes included in the Company’s Annual Report on Form 10-K for the year ended December 31, 2025, filed with the SEC on March 24, 2026.

In management’s opinion, the unaudited condensed consolidated financial statements reflect all adjustments (consisting of normal recurring adjustments) necessary to present fairly the financial position of the Company as of September 30, 2026, and results of operations and cash flows for all periods presented. The interim results presented are not necessarily indicative of results that can be expected for the full year ending December 31, 2026.

Use of Estimates

The preparation of the financial statements in accordance with U.S. GAAP requires management to make estimates and assumptions that affect the reported amounts of assets and liabilities and disclosure of contingent assets and liabilities at the date of the financial statements and the reported amounts of expenses during the reporting period. In preparing these financial statements, management used significant estimates in the following areas, among others: recoverability of the Company’s net deferred tax assets and related valuation allowance, useful lives and recoverability of property and equipment, determining the incremental borrowing rate for calculating lease liabilities and related right-of-use assets and finance lease assets, clinical trial accruals, accrual estimates for all contingent value rights (“CVRs”), andthe value attributed to employee stock options and other stock-based awards. On an ongoing basis, the Company reviews its estimates to ensure that they appropriately reflect changes in the business or as new information becomes available. Actual results may differ from these estimates.

Segment Information

The Company determines and presents operating segments based on the information internally provided to the Chief Operating Decision Makers (“CODMs”) in accordance with Accounting Standards Codification (“ASC”) 280, Segment Reporting. The Company’s CODMs are (i) the Chief Executive Officer and (ii) the President and Chief Financial Officer. The Company is a clinical-stage biotechnology company that operates as a single operating segment and hasone reportable segment. Refer to Note 13, Segment Information, for further information related to the Company’s segment.

Cash, Cash Equivalents and Investments

The Company considers all highly-liquid investments purchased with original maturities of 90 days or less at time of purchase to be cash equivalents. Cash and cash equivalents include cash held in banks and are stated at fair value.

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The following table provides a reconciliation of cash, cash equivalents, and restricted cash in the balance sheets that sum to the total of the same such amounts shown in the statements of cash flows (in thousands):

Cash equivalents consist of money market funds in which the carrying value equals the fair value (see Note 5, Fair Value of Financial Instruments). Restricted cash includes $0.3 million in cash deposits the Company maintains with its bank as collateral for the irrevocable letters of credit related to its lease obligations.

The Company’s investments in U.S. treasury notes are classified as held-to-maturity because the Company has the intent and ability to hold the securities to maturity. Accordingly, these securities are carried at amortized cost. Unrealized gains and losses are not recognized in other comprehensive income or loss.

Concentrations of Credit Risk

Financial instruments that subject the Company to significant concentrations of credit risk consist primarily of cash and cash equivalents. The Company’s cash and cash equivalent accounts, at times, may exceed federally insured limits. As of September 30, 2026, the Company had $78.8 million in excess of the federally insured limits. The Company places its cash in financial institutions that management believes to be of high credit quality.

Contingent Value Rights

In conjunction with the reverse merger, the Company entered into a CVR Agreement on December 18, 2023 with the Rights Agent named therein (the “CVR Agreement”) prior to Closing. Included in the CVR Agreement arethree different types of CVRs: (i) the Lease CVR, (ii) the Intellectual Property CVR, and (iii) the Sales Tax CVR (each as defined in the CVR Agreement). As of August 2025, the Sales Tax CVR was fully satisfied. The Company evaluated each of the CVRs to determine if they qualified as derivatives under ASC 815, Derivatives and Hedging, and concluded that since certain scope exceptions were met, the CVRs did not qualify as derivatives. Instead, the Company records a contingent consideration liability associated with the CVRs when payments are probable and estimable under ASC 450, Contingencies. In assessing whether payments are probable and estimable, the Company considers the existence of or ability to enter into agreements with third parties or government agencies and the timing of potential payments. Refer to Note 9, Commitments and Contingencies, for further discussion on the CVRs.

Income Taxes

The Company accounts for income taxes in accordance with ASC 740, Income Taxes, which prescribes the use of the liability method whereby deferred tax assets and liabilities are determined based on the difference between the financial statement and tax basis of assets and liabilities using enacted tax rates in effect for the year in which the differences are expected to reverse. A valuation allowance is provided to reduce the net deferred tax assets to a level which, more likely than not, will be realized. No provision for federal or state income taxes was recorded during the three and nine months ended September 30, 2026 and 2025, as the Company incurred operating losses and maintains a full valuation allowance against its net deferred tax assets.

The Company assesses its income tax positions and records tax benefits based upon management’s evaluation of the facts, circumstances, and information available at the reporting date. For those tax positions where it is more likely than not that a tax benefit will be sustained, the Company records the amount of tax benefit with a greater than 50 percent likelihood of being realized upon ultimate settlement with a taxing authority having full knowledge of all relevant information. For those income tax positions for which it is not more likely than not that a tax benefit will be sustained, no tax benefit is recognized in the financial statements. Potential interest and penalties associated with such uncertain tax positions is recorded as a component of income tax expense. As of September 30, 2026, there were no material changes to either the nature or the amounts of the uncertain tax positions.

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Significant Accounting Policies

The Company’s significant accounting policies are disclosed in the audited financial statements filed with the Company’s Annual Report on Form 10-K for the year ended December 31, 2025. Since the date of those financial statements, there have been no changes to the Company’s significant accounting policies.

Net Loss Per Share Attributable to Common Stockholders

Basic net loss per share of common stock is computed by dividing net loss attributable to the Company by the weighted-average number of shares of common stock outstanding during the period. In periods of losses, diluted net loss per share is computed on the same basis as basic net loss per share as the inclusion of any other potential shares outstanding would be anti-dilutive. Outstanding pre-funded warrants as of September 30, 2026 and 2025 were 7,459,225 and 6,792,559, respectively. Pre-funded warrants are considered outstanding as of their issuance date and are included in basic and diluted net loss per share because they are fully vested and exercisable for nominal cash consideration.

The following potentially dilutive securities have been excluded from the diluted per share calculations as they would be anti-dilutive:

Comprehensive Loss

Comprehensive loss consists of net loss and other comprehensive income (loss). The Company had no items of other comprehensive income (loss) during the three and nine months ended September 30, 2026 and 2025. Accordingly, comprehensive loss was equal to net loss for all periods presented.

Recently Issued Accounting Standards

From time to time, new accounting pronouncements are issued by the Financial Accounting Standards Board (“FASB”) or other standard setting bodies that the Company adopts as of the specified effective date. Unless otherwise discussed below, the Company does not believe that the adoption of recently issued standards has or may have a material impact on its condensed financial statements or disclosures.

Recently Issued Accounting Pronouncements Not Yet Adopted

In November 2024, the FASB issued ASU 2024-03, Income Statement - Reporting Comprehensive Income - Expense Disaggregation Disclosures(“ASU 2024-03”) which requires public entities to provide disaggregated disclosure of income statement expenses. Public entities are required to disaggregate, in a tabular presentation, each relevant expense caption on the face of the condensed consolidated statements of operations such as the following expenses: purchases of inventory, employee compensation, intangible asset amortization, and depreciation. In January 2025, the FASB issued ASU 2025-01, Income Statement - Reporting Comprehensive Income - Expense Disaggregation Disclosures, to clarify the effective date. The updated effective date for the Company to adopt ASU 2024-03 is for annual reporting periods beginning after December 15, 2026 and interim periods within annual reporting periods beginning after December 15, 2027, with early adoption permitted. The Company is currently evaluating the potential impact that ASU 2024-03 will have on its financial statement disclosures.

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In September 2025, the FASB issued ASU 2025-06, Intangibles - Goodwill and Other - Internal-Use Software (Subtopic 350-40)(“ASU 2025-06”) which removes all references to project stages throughout ASC 350-40, Intangibles — Goodwill and Other, Internal-Use Software. Cost capitalization will now begin solely when (1) management has authorized and committed to funding the software project, and (2) it is ‘probable’ the project will be completed and the software used to perform its intended function (referred to as the probable-to-complete recognition threshold). The effective date for the Company to adopt ASU 2025-06 is for annual reporting periods beginning after December 15, 2027 and interim reporting periods within those annual reporting periods, with early adoption permitted. The Company is currently evaluating the potential impact that ASU 2025-06 will have on its financial statement disclosures.

4. Investments

The following table summarizes the Company’s investment securities as of September 30, 2026 and December 31, 2025 (in thousands):

All of the Company’s investments mature within the next 12 months.

5. Fair Value of Financial Instruments

As of September 30, 2026 and December 31, 2025, financial assets measured at fair value on a recurring basis are categorized in the table below based upon the lowest level of significant input to the valuations (in thousands):

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Money market funds are cash equivalents and are included in cash and cash equivalents in the condensed consolidated balance sheet as of September 30, 2026 and December 31, 2025.

6. Prepaid Expenses and Other Current Assets

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

7. Property and Equipment, Net

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

The Company recorded depreciation and amortization expense of $0.8 million and $0.8 million for the three months ended September 30, 2026 and 2025, respectively, and recorded $2.4 million and $2.3 million for the nine months ended September 30, 2026 and 2025, respectively.

Management has reviewed its property and equipment for impairment whenever events and circumstances indicate that the carrying value of an asset might not be recoverable. During the nine months ended September 30, 2026, impairment losses were immaterial. During the nine months ended September 30, 2025, no impairment losses were recorded. Impairment losses are charged to research and development expenses in the condensed consolidated statement of operations. Fair value for the idle assets was determined by a quoted purchase price for the assets.

8. Accrued Expenses and Other Current Liabilities

Accrued expenses and other current liabilities consist of the following (in thousands):

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9. Commitments and Contingencies

Lease Obligations

New York Headquarters Lease

In September 2019, the Company commenced a sublease of approximately 6,000 square feet of office space for the corporate headquarters in New York, New York with a term expiring in June 2023.

In July 2021, the sublessor was released from the original lease by the landlord, and the Company attorned to the landlord the executory terms and provisions of the sublease. In February 2022, the Company entered into an extension of the New York office lease (retroactive to December 2021) through June 2026. In November 2025, the Company entered into a second amendment of the lease, extending the New York office lease through January 2028, with decreased monthly lease payments of approximately $0.03 million. As a result, the Company recorded an additional operating right-of-use asset of approximately $0.4 million and an additional operating lease liability of approximately $0.4 million.

Houston Lease

In August 2019, the Company entered into an agreement to lease approximately 26,905 square feet in Houston, Texas to build a manufacturing facility and office with a term expiring in August 2029. The Company has the option to renew the lease term fortwo additional five-year terms. The renewal periods were not included in the lease term for purposes of determining the lease liability or right-of-use asset. Monthly rent payments were approximately $0.03 million. In connection with the lease, the Company paid a security deposit of approximately $0.04 million.

In September 2020, the Company amended the lease agreement to further increase the rentable space to 42,342 square feet. The commencement date of the expansion space lease was January 1, 2021 and the monthly rent payments increased to a range of approximately $0.05 million to $0.06 million.

Blaine Lease in Seattle

As a result of the reverse merger, the Company assumed an operating lease for approximately 33,300 square feet of office space in Seattle, Washington for offices, a laboratory for research and development, and related uses. The lease expires on February 1, 2029, with the option to extend the lease fortwo five-year terms. The renewal periods were not included in the lease term for purposes of determining the lease liability or right-of-use asset.

Eastlake Lease in Seattle

As a result of the reverse merger, the Company assumed an operating lease for approximately 6,272 square feet of office space in Seattle, Washington for additional office and laboratory space for research and development and related uses (the “Eastlake Lease”). The Company had assumed the existing agreement to sublease the Eastlake Lease to an unrelated third party (“Eastlake Sublease”). Pursuant to the terms of the Eastlake Sublease, Neurogene received approximately $1.6 million in lease payments. The Eastlake Lease and the Eastlake Sublease each expired in accordance with their terms on September 30, 2026. The Company did not renew or extend either agreement, and no termination payments were made or received in connection with the expiration. The Company recorded sublease income of $0.1 million for the three months ended September 30, 2026 and 2025. The Company recorded sublease income of $0.4 million for the nine months ended September 30, 2026 and 2025. Sublease income is included in other income in the statement of operations. As of September 30, 2026, the Company had no remaining lease payments receivable under the Eastlake Sublease.

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Supplemental lease expense for the three and nine months ended September 30, 2026 and 2025 was as follows (in thousands):

Lease CVR

Under the CVR Agreement, each CVR holder is eligible to receive certain net savings, if any, realized by June 30, 2029, in connection with certain legacy lease obligations (the “Lease CVR”). As of September 30, 2026, approximately $0.4 million was recorded as a component of the contingent value rights liability on the Company’s condensed consolidated balance sheet consisting of lease commitments that were probable and estimable at the Closing. The commitments relate to Neoleukin’s sublease agreement, effective October 31, 2023, forone of its properties with an unrelated third party for the remainder of the lease term, which expired on September 30, 2026.

Intellectual Property CVR

Under the CVR Agreement, each CVR holder is eligible to receive 100% of the net proceeds, if any, derived from any consideration paid as a result of the disposition of Neoleukin’s pre-merger legacy assets pursuant to any agreements entered into before the Closing, and 80% of net proceeds, if any, derived from any consideration paid as a result of the disposition of Neoleukin’s pre-merger legacy assets pursuant to any agreements entered into withinone year after the Closing (the “Intellectual Property CVR”). Contingent consideration liabilities related to the CVR Agreement will only be recorded if the liabilities are probable and estimable as of the balance sheet date. Refer to the December 2023 CVR Licensing Agreement and April 2024 CVR Licensing Agreement subsections below for further detail on the current agreements related to the Company’s Intellectual Property CVR.

December 2023 CVR Licensing Agreement

Prior to the Closing, Neoleukin entered into a licensing agreement on December 13, 2023, with an unrelated third party to develop and commercialize certain legacy Neoleukin assets (the “December 2023 CVR Licensing Agreement”). In June 2024, an upfront payment of $0.2 million was received by the Company and was recorded as licensing revenue within the condensed consolidated statements of operations. Since the December 2023 CVR Licensing Agreement was entered into before the Closing, the CVR holders are eligible to receive 100% of the net proceeds derived from the December 2023 CVR Licensing Agreement. The December 2023 CVR Licensing Agreement contains development, regulatory and commercialization milestones totaling up to approximately $13.4 million, as well as royalty payments. However, as of September 30, 2026, no other development and sales milestones were achieved nor deemed probable of achievement under the December 2023 CVR Licensing Agreement.

April 2024 CVR Licensing Agreement

In April 2024, the Company entered into a licensing and intellectual property assignment agreement with another unrelated third party to develop and commercialize certain legacy Neoleukin assets (the “April 2024 CVR Licensing Agreement”). In April 2024, the Company received a one-time upfront payment of approximately $0.8 million and reimbursement of $0.01 million for patent expenses under the April 2024 CVR Licensing Agreement. Accordingly, the Company recorded $0.8 million as licensing revenue within the condensed consolidated statements of operations. Since the April 2024 CVR Licensing Agreement was entered into withinone year after the Closing, the CVR holders are eligible to receive 80% of the net proceeds derived from the April 2024 CVR Licensing Agreement. The April 2024 CVR Licensing Agreement contains development, regulatory and commercialization milestones totaling up to approximately $11.0 million, as well as royalty payments. However, as of September 30, 2026, no other development and sales milestones were achieved nor deemed probable of achievement under the April 2024 CVR Licensing Agreement.

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The December 2023 CVR Licensing Agreement and April 2024 CVR Licensing Agreement collectively account for the total Intellectual Property CVR. The total amount of $0.9 million due under the Intellectual Property CVR was offset by $0.4 million due to permitted deductions under the Merger Agreement and the remaining $0.5 million was paid to the CVR holders.

CVR Payments

In August 2025, the Company made the second CVR payment to CVR holders of $0.8 million. $0.4 million was applied to the Sales Tax CVR and $0.4 million was applied to the Lease CVR, reducing the respective liabilities. In February 2026, the Company made the third CVR payment to CVR holders of $0.6 million. $0.3 million was applied to the Intellectual Property CVR and $0.3 million was applied to the Lease CVR.

The following table summarizes the components of the contingent value rights liability in the condensed consolidated balance sheet as of September 30, 2026 and December 31, 2025 (in thousands):

As per the CVR Agreement, the total amount owed to CVR holders, after deductions permitted under the Merger Agreement, must be at least $0.5 million to trigger a CVR payment prior to the end of the CVR term.

All other payments under the CVR Agreement were not considered probable and estimable as of September 30, 2026 and therefore, no additional contingent consideration liability has been recorded. The Company will evaluate the probable and estimable range of outcomes under the CVR Agreement at each reporting period until the end of the CVR term and adjust the amounts accrued for, as necessary.

Employment Agreements

The Company has employment and consulting agreements with key personnel providing for compensation and severance in certain circumstances, as defined in the respective employment agreements.

Other Research and Development Arrangements

As of September 30, 2026, the Company had standing agreements with consultants, contractors or service providers that generally can be terminated by the Company with 30 to 60 days written notice, unless otherwise indicated.

Litigation and Legal Proceedings

The Company is subject to litigation and other claims that arise in the ordinary course of business. While the ultimate result of outstanding legal matters cannot presently be determined, the Company does not expect that the ultimate disposition will have a material effect on its financial condition, results of operations or cash flows. However, legal matters are inherently unpredictable and subject to significant uncertainties, some of which are beyond the Company’s control. As such, there can be no assurance that the final outcome of any particular legal matter will not have a material adverse effect on the Company’s financial condition, results of operations or cash flows.

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10. Licenses

Master Collaboration Agreement with The University of Edinburgh

In December 2020, the Company entered into a Master Collaboration Agreement (the “MCA”) with the University Court of the University of Edinburgh (the “University of Edinburgh”). Under the MCA, the Company and the University of Edinburgh agreed to collaborate on certain research and development projects (“Projects”), and the Company agreed to provide funding for such Projects for a 40-month initial term, which was extended in November 2023 for an additional 33 months and may befurther extended by mutual agreement. Under the MCA, the Company is obligated to pay semi-annual installment payments relating to funding of costs for personnel and lab consumables for the duration of the MCA. Either party may terminate the MCA for convenience upon 90 days’ notice. If the Company were to terminate the MCA, the Company would be responsible for all non-cancellable costs and commitments related to any particular Project and any and all funding costs for any person working on such Project.

License Agreement with The University of Edinburgh

In March 2022, the Company exercised an option under the MCA with respect to certain Projects and entered into a License Agreement with the University of Edinburgh (the “March 2022 Edinburgh License Agreement”), pursuant to which the Company licensed certain patents and know-how related to the EXACT technology and optimized MECP2 cassettes on an exclusive basis. Under the March 2022 Edinburgh License Agreement, the Company obtained an exclusive, worldwide license to the licensed patents to develop, manufacture, supply, sell, and commercialize any products that utilize the licensed patents (the “Licensed Products”) in exchange for low single-digit percentage royalties on future commercial net sales of the Licensed Products. Royalties are payable on a Licensed Product-by-Licensed Product and country-by-country basis until the later of the expiration of the last licensed patent covering such Licensed Product in the country where the Licensed Product is sold, or, if no licensed patent exists or has expired in such country, then 10 years from first commercial sale of such Licensed Product in such country (the “Royalty Term”). The term of the March 2022 Edinburgh License Agreement continues until the end of the Royalty Term and the expiration of all of the payment obligations under that license. The Company may terminate the March 2022 Edinburgh License Agreement for convenience upon 90 days’ notice. In connection with the license, the Company is also obligated to pay the University of Edinburgh up to $5.3 million in regulatory-related milestones, of which $0.3 million has been paid in connection with the Phase 1/2 study. The remaining regulatory milestone payments consist of $2.0 million payable upon achievement of the first regulatory approval (FDA or European Medicines Agency (“EMA”)) and $3.0 million payable upon achievement of the second regulatory approval (FDA or EMA). In addition, the Company may be obligated to make up to $25.0 million of sales-related milestone payments based on annual net sales of Licensed Products in excess of defined thresholds.

For the three months ended September 30, 2026 and 2025, the expense recorded by the Company related to the MCA was $0.4 million and $0.4 million, respectively. For the nine months ended September 30, 2026 and 2025, the expense recorded by the Company related to the MCA was $1.2 million and $1.2 million, respectively.

License Agreement with Virovek

In September 2020, the Company entered into a Non-Exclusive License Agreement with Virovek, Inc., pursuant to which the Company has a license to use certain patents andknow-how on a non-exclusive basis related to the Company’s baculovirus process in exchange for low single-digit percentage royalties on future commercial net sales of each product using the baculovirus process, development milestone payments of up to$0.2 millionin the aggregate, and a nonrefundable annual license fee. This agreement continues until the later of (i) the expiration of the last to expire patent right that covers the manufacture, use, offer for sale, sale, importation, export or supply of any licensed product, (ii)ten years after the first commercial sale of any licensed product, or (iii) the expiration of all regulatory or market exclusivities. The Company may terminate this agreement for convenience upon 60 days’ notice. During the nine months ended September 30, 2026 and 2025, no milestone expense was recorded.

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License Agreement with Sigma-Aldrich Co

In January 2023, the Company entered into a Non-Exclusive License Agreement with Sigma-Aldrich Co. LLC, pursuant to which the Company has a license to certain patents and know-how on a non-exclusive basis related to certain cell lines used in the Company’s baculovirus process in exchange for a small annual fee on a product-by-product basis, payable once the first product candidate enters the clinic. In addition, on a product-by-product basis, the Company is obligated to pay up to$2.5 millionin the aggregate for regulatory-related milestones. This agreement remains in force for as long as the Company continues to possess and use the licensed technology. The Company may terminate this agreement for convenience upon 60 days’ notice. During the nine months ended September 30, 2026 and 2025, no milestone expense was recorded.

License Agreement with Stanford

In August 2024, the Company entered into a Non-Exclusive License Agreement with the Board of Trustees of Leland Stanford Junior University (the “Stanford License Agreement”) to license, on a non-exclusive basis, certain biological materials used in the manufacturing process of the Company’s product candidates, including NGN-401. Over the 10-year term of the Stanford License Agreement, the Company is obligated to pay an annual license maintenance fee. The Company may terminate this agreement for convenience upon 30 days’ notice. During the nine months ended September 30, 2026 and 2025, no milestone expense was recorded.

11. Stockholders’ Equity

Common Stock and Pre-funded Warrants

In April 2025, the Company entered into an exchange agreement with existing stockholders to exchange an aggregate of 667,500 shares of the Company’s common stock for pre-funded warrants to purchase an aggregate of 667,563 shares of the Company’s common stock at an exercise price of $0.001 per share. The exchange was executed to facilitate the investor’s beneficial ownership thresholds. The exchange was accounted for as an equity-for-equity transaction. The Company derecognized the common shares and recognized an equivalent value in pre-funded warrants, with no gain or loss recognized.

At-The-Market Offering of Shares

In August 2025, the Company entered into an at-the-market (“ATM”) sales agreement (the “Sales Agreement”) with Leerink Partners LLC (“Leerink”), as sales agent, pursuant to which the Company may offer and sell, from time to time, shares of the Company’s common stock with an aggregate price up to $150.0 million through Leerink. During the nine months ended September 30, 2026, the Company sold 889,054 shares of the Company’s common stock pursuant to the Sales Agreement, and received $31.8 million in net proceeds after deducting commissions and other offering expenses. As of September 30, 2026, the remaining amount authorized for sale under the Sales Agreement was $86.2 million.

In connection with the Sales Agreement, the Company incurred approximately $0.9 million of offering costs, of which $0.2 million was deferred. The deferred offering costs are recognized ratably as a reduction to additional paid-in-capital as shares are sold under the Sales Agreement. As of September 30, 2026, approximately $0.1 million of deferred offering costs remained on the balance sheet.

Public Offering of Common Stock and Pre-funded Warrants

In July 2026, the Company issued and sold an aggregate of 4,124,999 shares of its common stock (inclusive of 624,999 shares of common stock pursuant to the exercise in full of the underwriters’ option to purchase additional shares) at a public offering price of $30.00 per share and, in lieu of common stock to certain investors, pre-funded warrants to purchase up to 666,666 shares of the Company’s common stock at a public offering price of $29.999999 per pre-funded warrant. The Company received net proceeds of approximately $134.9 million, after deducting the underwriters’ discount and commissions and offering expenses.

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Pre-funded Warrants

The Company has pre-funded warrants outstanding to purchase an aggregate of 7,459,225 shares of the Company’s common stock as of September 30, 2026. The pre-funded warrants are exercisable at any time for exercise prices ranging from $0.000001 to $0.001, except that the pre-funded warrants cannot be exercised by a holder if, after giving effect thereto, such holder would beneficially own more than 4.99% or 9.99% of the Company’s outstanding common stock, at the holder’s election and subject to certain exceptions. However, any holder may increase or decrease such percentage to any other percentage (not in excess of 19.99%) upon at least 61 days’ prior notice from the holder to the Company. The holders of the pre-funded warrants will not have the right to vote the shares underlying the pre-funded warrants on any matter except to the extent required by Delaware law. These warrants are classified as equity. Information on the outstanding warrants is as follows:

The Company had reserved shares of the Company’s common stock for future issuance as follows:

12. Stock-Based Compensation

In March 2025, the Company’s board of directors approved the Neurogene Inc. 2025 Inducement Plan, which reserves for issuance up to 500,000 shares of the Company’s common stock underlying inducement awards. In August 2026, the Company’s board of directors approved an increase of 548,000 shares reserved for issuance under the Company’s 2025 Inducement Plan. The additional shares will be available for future equity awards granted pursuant to the terms of the 2025 Inducement Plan.

The Company measures stock-based awards at their grant-date fair value and records compensation expense on a straight-line basis over the vesting period of the awards. The Company recorded stock-based compensation expense in the following expense categories in its accompanying condensed consolidated statements of operations (in thousands):

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The following table summarizes the option activity:

As of September 30, 2026, the aggregate intrinsic value of outstanding options and exercisable options was approximately $21.9 million and $8.8 million, respectively. The aggregate intrinsic value of options exercised was $1.5 million for the nine months ended September 30, 2026.

The weighted-average grant date fair value of options granted was $17.00 and $13.43 per share for the nine months ended September 30, 2026 and 2025, respectively. The Company recorded stock-based compensation related to stock options of approximately $3.4 million and $2.2 million for the three months ended September 30, 2026 and 2025, respectively. The Company recorded stock-based compensation related to stock options of approximately $9.0 million and $6.3 million for the nine months ended September 30, 2026 and 2025, respectively. As of September 30, 2026, the total unrecognized compensation expense related to unvested stock option awards was approximately $27.8 million, which the Company expects to recognize over a weighted-average period of 2.77 years.

The fair value of each option was estimated on the grant date using the weighted-average assumptions in the table below:

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Restricted Stock Units

A summary of the Company’s restricted stock unit (“RSU”) activity and related information for the nine months ended September 30, 2026 is as follows:

The Company recorded stock-based compensation expense related to RSUs of approximately $0.9 million and $0.7 million for the three months ended September 30, 2026 and 2025, respectively. The Company recorded stock-based compensation expense related to RSUs of approximately $2.6 million and $2.1 million for the nine months ended September 30, 2026 and 2025, respectively. As of September 30, 2026, there was approximately $3.9 million of unrecognized compensation cost related to unvested RSUs, which is expected to be recognized over a remaining weighted average vesting period of approximately 1.70 years.

Performance Stock Units

A summary of the Company’s performance stock unit (“PSU”) activity and related information for the nine months ended September 30, 2026 is as follows:

The PSUs were granted with vesting intwo equal tranches based on certain performance conditions. Each PSU entitles the holder to receiveone share of the Company's common stock when the PSU vests. Stock-based compensation expense for PSUs will be recognized when it is probable that the performance conditions will be achieved. During 2025, the performance conditions underlying the first tranche of 126,062 PSUs were achieved for the first milestone and are currently considered probable to vest. As of September 30, 2026, the performance conditions underlying the second tranche of 126,062 PSUs were deemed probable of achievement and considered probable to vest. The Company recorded stock-based compensation expense related to PSUs of approximately $0.8 million and $0.4 million for the three months ended September 30, 2026 and 2025, respectively. The Company recorded stock-based compensation expense related to PSUs of approximately $5.0 million and $2.4 million for the nine months ended September 30, 2026 and 2025, respectively. As of September 30, 2026, there was approximately $1.4 million of unrecognized compensation cost related to PSUs, which is expected to be recognized over a remaining weighted average vesting period of approximately 0.45 years.

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2023 Employee Stock Purchase Plan

For the nine months ended September 30, 2026, the Company issued 3,815 shares of common stock at a purchase price of $17.65 per share under the 2023 Employee Stock Purchase Plan. Cash received from the purchases under the plan for the nine months ended September 30, 2026 was approximately $0.1 million.

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13. Segment Information

Operating segments are defined as components of an entity for which separate financial information is available and that is regularly reviewed by the CODMs in deciding how to allocate resources and in assessing performance. The Company’s CODMs are (i) the Chief Executive Officer and (ii) the President and Chief Financial Officer. The Company is a clinical-stage biotechnology company that operates as a single operating segment and hasone reportable segment. In addition to reviewing the expenses in the consolidated statement of operations, the CODMs are provided with research and development costs for Rett syndrome, Batten disease and Early Discovery, as well as categorized general and administrative expenses. The research and development programs are considered significant by the Company. The CODMs assess the financial performance of the segment and decide how to allocate resources based on net loss on a consolidated basis. The measure of segment assets is reported on the condensed consolidated balance sheets as total consolidated assets. The CODMs also assess performance of the segment according to preclinical and clinical data, the stage of development of the research and development programs, along with program specific expenses and market conditions in the pharmaceutical and biotechnology sectors.

As of September 30, 2026 and 2025, the Company did not have any significant long-lived assets located outside of the United States. Information on the segment and reconciliation to net loss is as follows (in thousands):

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