Voyager Therapeutics, Inc.

1. Nature of business

Voyager Therapeutics, Inc. (the “Company”) is a biotechnology company whose mission is to leverage the power of human genetics to modify the course of and ultimately cure neurological diseases. Its pipeline includes programs for Alzheimer’s disease, Friedreich’s ataxia, Parkinson’s disease, and multiple other diseases of the central nervous system (“CNS”). Its pipeline includes programs it wholly owns and programs it is advancing with licensees and collaborators, including Alexion, AstraZeneca Rare Disease; Novartis Pharma AG (“Novartis”); Neurocrine Biosciences, Inc. (“Neurocrine”); and Transition Bio, Inc.

Many of the Company’s programs are derived from its TRACER™ (Tropism Redirection of AAV by Cell-type-specific Expression of RNA) adeno-associated virus (“AAV”) capsid discovery platform, which it has used to generate novel capsids and identify associated receptors to potentially enable high brain penetration with genetic medicines following intravenous dosing. TRACER is a broadly applicable, RNA-based screening platform that enables rapid discovery of AAV capsids with robust penetration of the blood-brain barrier (“BBB”) and enhanced CNS tropism in multiple species, including non-human primates. The Company is also developing a second, non-viral platform focused on non-viral receptor-mediated transport across the BBB, the Voyager NeuroShuttle TM platform.

The Company has a history of incurring annual net operating losses. As of September 30, 2026, the Company had an accumulated deficit of $523.0 million. The Company has not generated any product revenue and has financed its operations primarily through public offerings and private placements of its equity securities and funding from fees, milestone payments, and cost reimbursements associated with its prior and current collaborations and license agreements.

As of September 30, 2026, the Company had cash, cash equivalents, and marketable securities of $132.1 million. Based upon its current operating plan, the Company expects that its existing cash, cash equivalents, and marketable securities at September 30, 2026, to be sufficient to meet the Company’s planned operating expenses and capital expenditure requirements for at least twelve months from the issuance of these condensed consolidated financial statements.

There can be no assurance that the Company will be able to obtain additional debt or equity financing on terms acceptable to the Company or generate product revenue or revenue from collaboration partners, on a timely basis or at all. The failure of the Company to obtain sufficient funds on acceptable terms when needed could have a material adverse effect on the Company’s business, results of operations, and financial condition and require the Company to defer or limit some or all of its research, development and/or clinical programs.

2. Summary of significant accounting policies and basis of presentation

Basis of Presentation

The accompanying unaudited condensed consolidated financial statements of the Company have been prepared in accordance with accounting principles generally accepted in the United States (“GAAP”) for interim financial reporting. Accordingly, they do not include all of the information and footnotes required by GAAP for complete financial statements. For further information, refer to the consolidated financial statements and footnotes included in the Company’s Annual Report on Form 10-K for the fiscal year ended December 31, 2025, as filed with the Securities and Exchange Commission on March 9, 2026. These interim condensed consolidated financial statements, in the opinion of management, reflect all normal recurring adjustments necessary for a fair presentation of the Company’s financial position and results of operations for the periods presented. Any reference in these notes to applicable guidance is meant to refer to the authoritative GAAP, which can be found in the Accounting Standards Codification and Accounting Standards Updates of the Financial Accounting Standards Board.

Principles of Consolidation

The unaudited interim condensed consolidated financial statements include the accounts of the Company and its wholly-owned subsidiary as disclosed in Note 2, Summary of significant accounting policies and basis of presentation, within the “Notes to Consolidated Financial Statements” accompanying the Company’s Annual Report on Form 10-K for the fiscal year ended December 31, 2025. Intercompany balances and transactions have been eliminated.

Use of Estimates

The preparation of condensed consolidated financial statements in conformity with GAAP requires management to make estimates and assumptions that affect the amounts reported in the condensed consolidated financial statements and accompanying notes. On an ongoing basis, the Company’s management evaluates its estimates, which include, but are not limited to, estimates related to revenue recognition, research and development accrued expenses, stock‑based compensation expense, and income taxes. The Company bases its estimates on historical experience and other market-specific or other relevant assumptions that it believes to be reasonable under the circumstances. Actual results may differ from those estimates or assumptions.

Summary of Significant Accounting Policies

There have been no changes in the Company’s significant accounting policies as described in Note 2, Summary of significant accounting policies and basis of presentation, within the “Notes to Consolidated Financial Statements” accompanying the Company’s Annual Report on Form 10-K for the fiscal year ended December 31, 2025.

3. Fair value measurements

Assets and liabilities measured at fair value on a recurring basis as of September 30, 2026 and December 31, 2025, are as follows:

The Company measures the fair value of money market funds, U.S. Treasury notes and U.S. Government agency securities based on quoted prices in active markets for identical securities. The Company measures the fair value of the Level 2 securities, including corporate bonds and commercial paper, based on recent trades of securities in inactive markets or based on quoted market prices of similar instruments and other significant inputs derived from or corroborated by observable market data.

4. Cash equivalents and available-for-sale marketable securities

Cash equivalents and available-for-sale marketable securities included the following as of September 30, 2026 and December 31, 2025:

All of the Company’s marketable securities as of September 30, 2026 and December 31, 2025, have a contractual maturity oftwo years or less.

The Company reviews investments whenever the fair value of an investment is less than the amortized cost and evidence indicates that an investment’s carrying amount is not recoverable within a reasonable period of time. In connection with these investments, the Company evaluates whether the decline in fair value has resulted from credit losses or other factors, considering the extent to which fair value is less than amortized cost, any changes to the rating of the security by a rating agency, and adverse conditions specifically related to the security, among other factors. If this assessment indicates that a credit loss exists, the present value of cash flows expected to be collected from the security is compared to the amortized cost basis of the security. If the present value of cash flows expected to be collected is less than the amortized cost basis, a credit loss exists and an allowance for credit losses is recorded on the condensed consolidated balance sheet, limited by the amount that the fair value is less than the amortized cost basis. Any impairment that is not related to credit is recognized in other comprehensive (loss) income. Changes in the allowance for credit losses are recorded as a provision for (or reversal of) credit loss expense in other income, net within the condensed consolidated statement of operations and comprehensive (loss) income. Losses are charged against the allowance when the Company believes the uncollectability of an available-for-sale security is confirmed or when either of the criteria regarding intent or requirement to sell is met. No credit losses were recorded during the periods presented.

As of September 30, 2026 and December 31, 2025, the Company held 59 and 20 marketable securities, respectively, that were in an unrealized loss position, representing $78.4 million and $26.6 million in fair value, respectively. The unrealized losses as of September 30, 2026 and December 31, 2025, were attributable to changes in interest rates and do not represent credit losses. The Company does not intend to sell these securities, and it is not more likely than not that it will be required to sell them before recovery of their amortized cost basis.

The following table provides a reconciliation of cash, cash equivalents, and restricted cash within the condensed consolidated balance sheets that sum to the total of the same amounts shown in the condensed consolidated statements of cash flows:

Restricted cash balances for both periods presented are held in the form of money market accounts and represent collateral for the Company’s facility lease obligations.

5. Accrued expenses

Accrued expenses as of September 30, 2026 and December 31, 2025, consist of the following:

During the three and nine months ended September 30, 2026, the Company recognized $1.4 million of employee separation costs related to restructuring activities, which are included within “employee compensation costs” above.

6. Lease obligation

Operating Leases

As of September 30, 2026, the Company has a lease for laboratory and office space at 75 Hayden Avenue in Lexington, Massachusetts (the “Lexington Facility”) through January 31, 2031, and a lease for additional office and laboratory space at 64 Sidney Street in Cambridge, Massachusetts (the “Cambridge Facility”) through November 30, 2026.

In August 2023, the Company entered into a first amendment (the “First Amendment”) to its existing lease for the Lexington Facility, pursuant to which the Company agreed to lease approximately 61,307 square feet of additional office and laboratory space. The commencement date for the First Amendment occurred on February 1, 2024. The expected contractual obligation under the First Amendment to the Company’s existing lease for the Lexington Facility is approximately $35.4 million, to be paid over the 7-year term of the lease.

The Company’s lease agreements require the Company to maintain a cash deposit or irrevocable letter of credit in the aggregate amount of $2.7 million payable to its landlords as security for the performance of its obligations under the leases. These amounts are recorded as restricted cash in the accompanying condensed consolidated balance sheets.

In August 2024, the Company executed the sublease of the Cambridge Facility (the “Sublease Agreement”). Payments received under the Sublease Agreement are included in other income in the condensed consolidated statements of operations and comprehensive loss. Subject to certain conditions set forth therein, the Sublease Agreement terminates simultaneously with the Company’s lease for the Cambridge Facility.

Operating lease cost was $1.8 million and $1.9 million during the three months ended September 30, 2026 and 2025, respectively. Operating lease cost was $5.5 million and $5.7 million during the nine months ended September 30, 2026 and 2025, respectively. As of September 30, 2026, the weighted-average remaining lease term was 2.9 years and the weighted-average incremental borrowing rate used to determine the operating lease liability was 6.5%.

The following table summarizes the operating sublease income generated under the Sublease Agreement for thethree and nine months ended September 30, 2026 and 2025:

Future minimum lease payments due under operating leases are as follows:

7. Commitments, contingencies and other liabilities

Other Agreements

In 2016, the Company entered into a research and development funding arrangement with a non-profit organization that provided up to $4.0 million in funding to the Company upon the achievement of certain clinical and development milestones. The agreement, as amended in 2022, provides that the Company is obligated to repay amounts received under certain circumstances, including termination of the agreement, and to pay an amount up to 2.6 times the funding received upon successful development and commercialization of any products developed. In 2017, the Company earned a milestone payment of $1.0 million. The Company evaluated the arrangement and concluded that it represents a research and development financing arrangement as it is probable that the Company will repay amounts received under the arrangement. As a result, the $1.0 million is recorded as a non-current liability in the condensed consolidated balance sheet.

Litigation

The Company was not a party to any material legal matters or claims as of September 30, 2026 or December 31, 2025. The Company didnot have contingency reserves established for any litigation liabilities as of September 30, 2026 or December 31, 2025.

8. Significant agreements

The Company’s significant agreements are described in Note 9, Significant Agreements, within the “Notes to Consolidated Financial Statements” accompanying the Company’s Annual Report on Form 10-K for the fiscal year ended December 31, 2025. During the three and nine months ended September 30, 2026, there were no material changes to the Company’s collaboration agreements or option and license agreements, and the Company did not enter into any new material collaboration or license agreements. The Company recorded collaboration revenue of $4.0 million and $13.4 million during the three months ended September 30, 2026 and 2025, respectively. The Company recorded collaboration revenue of $9.8 million and $25.0 million during the nine months ended September 30, 2026 and 2025, respectively.

Related Party Collaboration Receivable and Deferred Revenue

The following table presents changes in the balances of the Company’s related party collaboration receivable and contract liabilities (reflected as deferred revenue in the condensed consolidated balance sheets) for the collaboration and license agreement the Company entered into with Neurocrine in January 2023 (the “2023 Neurocrine Collaboration Agreement”) and the collaboration and license agreement the Company entered into with Neurocrine in January 2019 (the “2019 Neurocrine Collaboration Agreement”) during the nine months ended September 30, 2026:

The change in the related party collaboration receivable balance for the nine months ended September 30, 2026, is primarily driven by amounts owed to the Company for research and development services provided, offset by amounts collected during the period, under the 2023 and 2019 Neurocrine Collaboration Agreements. Deferred revenue activity for the nine months ended September 30, 2026, includes the recording of $1.6 million of collaboration revenue recognized on the proportional performance model during the period for the 2023 and 2019 Neurocrine Collaboration Agreements.

9. Stock‑based compensation

Stock‑Based Compensation Expense

Total compensation cost recognized for all stock‑based compensation awards in the condensed consolidated statements of operations and comprehensive loss was as follows:

Employee Stock Purchase Plan

In October 2015, the Company’s board of directors (the “Board”) and stockholders approved the 2015 Employee Stock Purchase Plan (the “2015 ESPP”). Under the 2015 ESPP, all full-time employees of the Company are eligible to purchase common stock of the Company twice per year, at the end of eachsix-month payment period. During each payment period, eligible employees who so elect, may authorize payroll deductions in an amount of 1% to 10% (whole percentages only) of the employee’s base pay for each payroll period. At the end of each payment period, the accumulated deductions are used to purchase shares of common stock from the Company at a discount. A total of 262,362 shares of common stock were initially authorized for issuance under the 2015 ESPP.

On March 18, 2025, the Board adopted, and on June 3, 2025, the stockholders approved, the Amended and Restated 2015 Employee Stock Purchase Plan (together with the 2015 ESPP, the “ESPP”) to (i) eliminate the evergreen provision in the 2015 ESPP and (ii) expand the class of eligible employees by eliminating the requirement that participants must have completed six months of employment.

As of September 30, 2026, there were 1,736,020 shares available for future purchase under the ESPP.

2025 Stock Incentive Plan

On March 18, 2025, the Board adopted, and on June 3, 2025, the stockholders approved, the 2025 Stock Incentive Plan (the “2025 Plan”). Under the 2025 Plan, the Company may issue awards for up to a number of shares of common stock equal to the sum of: (i)3,631,952 shares of common stock; and (ii) such additional number of shares of common stock (up to 14,190,976 shares)as is equal to the sum of (x) the number of shares of common stock reserved for issuance under the Company’s 2015 Stock Option and Incentive Plan (the “2015 Plan”) that remained available for grant thereunder immediately prior to the date that the 2025 Plan was approved by the Company's stockholders and (y) the number of shares of common stock subject to awards granted under the 2015

Plan that were outstanding as of the date that the 2025 Plan was approved by the Company's stockholders and which awards expire, terminate or are otherwise surrendered, cancelled, forfeited or repurchased by the Company at their original issuance price pursuant to a contractual repurchase right (subject, however, in the case of incentive stock options, to any limitations under the Internal Revenue Code of 1986, as amended, and any regulations thereunder).

The Company intends to utilize the 2025 Plan to grant equity awards to the Company’s employees, non-employee directors, consultants, and advisors in order to recruit, incentivize, retain and reward those who are critical to the Company’s success. No new awards will be granted under the 2015 Plan.

As of September 30, 2026, there were 5,636,483 shares available under the 2025 Plan.

Restricted Stock Units and Performance Restricted Stock Units

A summary of the status of and changes in unvested restricted stock unit (“RSU”) activity and performance-based restricted stock unit (“PRSU”) activity under the Company’s equity award plans for thenine months ended September 30, 2026, was as follows:

All RSUs granted during the nine months ended September 30, 2026, vest in equal amounts, annually over three years. Stock-based compensation for RSUs is based on the fair value of the Company’s common stock on the date of grant and is recognized over the vesting period.

As of September 30, 2026, the Company had unrecognized stock-based compensation expense related to its unvested RSUs (excluding PRSUs) of $3.9 million, which is expected to be recognized over the remaining average vesting period of 1.8 years.

During the first quarter of 2025, in connection with the Company’s annual compensation cycle, the Company granted PRSUs to members of the Company’s senior leadership team to more closely align with long-term performance incentives. The awards vest as to a certain number of PRSUs upon the achievement of specified clinical performance milestones over multiple years. Stock-based compensation for PRSUs is based on the fair value of the Company’s common stock on the date of grant and will be recognized at the time the achievement of the specified performance milestones becomes probable. The Company did not recognize any stock-based compensation expense in connection with the PRSUs during the nine months ended September 30, 2026.

As of September 30, 2026, the Company had unrecognized stock-based compensation expense related to its unvested PRSUs of $2.0 million. The Company will recognize a cumulative catch-up adjustment in the period in which the specified performance condition is considered probable.

Stock Options

The following is a summary of stock option activity for thenine months ended September 30, 2026:

As of September 30, 2026, the Company had unrecognized stock-based compensation expense related to its unvested stock options of $9.0 million, which is expected to be recognized over the remaining weighted-average vesting period of 2.4 years.

10. Net loss per share

For purposes of the diluted net loss per share, unvested restricted common stock awards, unvested RSUs and PRSUs, and outstanding stock options are considered to be potentially dilutive securities. Unvested RSUs and PRSUs and outstanding stock options were excluded from the calculation of diluted net loss per share in the three and nine months ended September 30, 2026 and 2025, because their effect would be anti-dilutive and therefore, basic and diluted net loss per share were the same for the three and nine months ended September 30, 2026 and 2025.

The following table sets forth the outstanding potentially dilutive securities that have been excluded in the calculation of diluted net loss per share because to include them would be anti-dilutive:

11. Related party transactions

During the three and nine months ended September 30, 2026, the Company received scientific advisory and consulting services from one of its prior executives, Dinah Sah, Ph.D., the Company’s former Chief Scientific Officer. The total amount of fees paid to Dr. Sah for services provided during the three months ended September 30, 2026 and 2025 was $0.1 million and $0.1 million, respectively. The total amount of fees paid to Dr. Sah for services provided during each of the nine months ended September 30, 2026 and 2025 was $0.4 million.

Under both the 2019 Neurocrine Collaboration Agreement and the 2023 Neurocrine Collaboration Agreement, the Company and Neurocrine have agreed to conduct research, development and commercialization activities for certain of the Company’s AAV gene therapy product candidates. Any amounts due from Neurocrine are reflected as related party collaboration receivable. Amounts received from Neurocrine that have not yet been recognized as revenue are reflected as deferred revenue. Refer to Note 8 for further description of these account balances.

For the three months ended September 30, 2026 and 2025, the Company recognized collaboration revenue of $0.5 million and $11.8 million, respectively, related to the 2023 and 2019 Neurocrine Collaboration Agreements. For the nine months ended September 30, 2026 and 2025, the Company recognized collaboration revenue of $2.2 million and $20.4 million, respectively, related to the 2023 and 2019 Neurocrine Collaboration Agreements.

12. Segment Information

The Company’s Chief Operating Decision Maker (“CODM”), the Company’s Chief Executive Officer, views the Company’s operations and manages its business as asingle operating segment, which is the business of developing and commercializing genetic medicines. The Company therefore hasone reportable segment.

The CODM reviews the segment’s profit or loss based on net loss reported on the condensed consolidated statement of operations and comprehensive loss and considers forecast-to-actual variances quarterly for expenses that are deemed significant in making resource allocation decisions and assessing performance. Further, the CODM reviews the segment’s assets based on total assets reported on the condensed consolidated balance sheets. All long-lived assets are held in the United States.

The CODM views specific categories within research and development expenses and general and administrative expenses in totality as significant. Further, the CODM views the external research and development expenses of specific programs as significant given the impact on achieving the Company’s corporate goals. The following table reconciles reported collaboration revenue and segment expenses to net loss under the significant expense principle for thethree and nine months ended September 30, 2026 and 2025:

(1)

External research and development is allocated to the Company’s programs and platforms and includes laboratory supplies and non-employee consultant and contractor costs.

(2)

Partnered programs include programs in which the Company is collaborating with partners to develop AAV gene therapy products and product candidates under the Company’s 2019 and 2023 Neurocrine Collaboration Agreements and the License and Collaboration Agreement the Company entered into with Novartis on December 28, 2023.

(3)

Other programs and platforms consist of expenses related to other early research programs and platforms that are not considered quantitatively and qualitatively significant, including capsid discovery, non-viral delivery, and early research programs.

(4)

Internal research and development consists of employee-related expenses, including salaries, benefits, and stock-based compensation expense.

(5)

Depreciation and amortization expense is allocated between general and administrative and facilities and other research and development.