Amylyx Pharmaceuticals, Inc.

(unaudited)

1. Nature of the Business

Amylyx Pharmaceuticals, Inc., together with its wholly-owned subsidiaries, known as Amylyx or the Company, is a pre-commercial pharmaceutical company with a mission to develop novel therapies for communities with high unmet medical needs. The Company has nonclinical and clinical development programs underway in endocrine conditions and neurodegenerative diseases. The Company is currently developing four investigational therapies for potential impact across several diseases: avexitide in PBH, AMX0318 in PBH and other rare diseases, AMX0035 in Wolfram syndrome, and AMX0114 in ALS.

Risks and Uncertainties

The Company is subject to risks and uncertainties common to companies in the biotechnology industry, including, but not limited to, the outcome of nonclinical studies and clinical trials, potential difficulties with or delays in timing with respect to regulatory approval processes, development by competitors of new technological innovations, dependence on key personnel, protection of proprietary technology, compliance with government regulations, ability to secure additional capital to fund operations, and risks associated with the economic challenges caused by economic uncertainty in various global markets caused by geopolitical instability and conflict. The Company and its contractors may also experience disruptions in supply of its products, if approved, or its current or future product candidates and other items that are essential for its research, development, and commercialization activities.

2. Summary of Significant Accounting Policies

Significant Accounting Policies

The Company’s significant accounting policies are disclosed in the audited consolidated financial statements for the year ended December 31, 2025 and the notes thereto, which are included in the Company’s most recent Annual Report on Form 10-K. There have been no material changes to its significant accounting policies since the date of those consolidated financial statements.

Basis of Presentation and Consolidation

The accompanying condensed consolidated financial statements and the related interim disclosures are unaudited and have been prepared in conformity with accounting principles generally accepted in the U.S., or GAAP, and pursuant to the rules and regulations of the SEC for the interim financial information. These unaudited condensed consolidated financial statements include the accounts of the Company and its wholly owned subsidiaries. All intercompany balances and transactions have been eliminated in consolidation. Certain information and footnote disclosures normally included in financial statements prepared in accordance with GAAP have been condensed or omitted as permitted by the SEC’s rules and regulations for interim reporting. Interim period results are not necessarily indicative of results of operations or cash flows for a full year or any subsequent interim period. The accompanying unaudited condensed consolidated financial statements should be read in conjunction with the audited consolidated financial statements and notes included in the Company’s Annual Report on Form 10-K for the year ended December 31, 2025.

In the opinion of the Company’s management, all normal and recurring adjustments necessary for a fair presentation have been reflected. Any reference in these notes to applicable guidance is meant to refer to the authoritative GAAP as found in the ASC, and Accounting Standards Update, or ASU, of the Financial Accounting Standards Board, or FASB.

Use of Estimates

The preparation of the condensed consolidated financial statements in conformity with GAAP requires the Company’s management to make estimates and assumptions that affect the reported amounts of assets and liabilities at the date of the financial statements and the reported amount of expenses during the reporting period. Actual results could differ from those estimates. Management considers many factors in selecting appropriate financial accounting policies in developing the estimates and assumptions that are used in the preparation of the financial statements. Management must apply significant judgment in this process. Management’s estimation process often may yield a range of potentially reasonable estimates and management must select an amount that falls within that range of reasonable estimates.

New Accounting Pronouncements Not Yet Adopted

In November 2024, the FASB issued ASU No. 2024-03, Income Statement – Reporting Comprehensive Income – Expense Disaggregation Disclosures (Subtopic 220-40): Disaggregation of Income Statement Expenses, which requires new financial statement disclosures in tabular format, in the notes to financial statements, of specified information about certain costs and expenses. The amendments in this update do not change or remove current expense disclosure requirements. The amendments in this update are effective for the Company's annual financial statement disclosure beginning December 31, 2027, and interim periods within the years beginning January 1, 2028. Early adoption is permitted. The Company is currently evaluating the impact of this ASU on its consolidated financial statements and related disclosures.

3. MARKETABLE SECURITIES

The Company has classified all of its marketable securities at September 30, 2026 as “available-for-sale”. The Company considers its available-for-sale portfolio as available for use in current operations. Accordingly, those marketable securities with contractual maturities greater than one year from the date of purchase are classified as current assets on the accompanying balance sheets. The Company records available-for-sale securities at fair value, with the unrealized gains and losses included as a separate component of other accumulated comprehensive loss. There wereno realized gains or losses recognized during thethree and nine months ended September 30, 2026 and 2025.

The Company adjusts the cost of available-for-sale debt securities for amortization of premiums and accretion of discounts to maturity. Such amortization and accretion are included in interest income. The cost of securities sold is based on the specific identification method. The Company includes interest and dividends on securities classified as available-for-sale in interest income. Accrued interest receivable relating to the Company’s available-for-sale securities is presented within prepaid expenses and other current assets in the accompanying condensed consolidated balance sheets, and amounted to$2.9 million and$0.1 million at September 30, 2026 and December 31, 2025, respectively.

As of September 30, 2026, there wereno securities in an unrealized loss position for greater than 12 months. The Company does not intend to sell the investments and it is not more likely than not that the Company will be required to sell the investments before recovery of their amortized cost bases. The Company did not record an allowance for credit losses as of September 30, 2026. The contractual maturities of the Company's available-for-sale marketable securities range from less than one year to three years.

Marketable securities, which are classified as available-for-sale, consisted of the following (in thousands):

4. Accrued Expenses

Accrued expenses consisted of the following (in thousands):

5. FAIR VALUE MEASUREMENTS

The following tables present information about the Company’s financial assets and liabilities measured at fair value on a recurring basis and indicates the level of the fair value hierarchy utilized to determine such fair values (in thousands):

The Company classifies its cash equivalents, treasury bills, and treasury notes as Level 1 assets under the fair value hierarchy, as these assets have been valued using quoted market prices for identical assets in active markets without any valuation adjustment. The Company classifies its commercial paper as Level 2 assets under the fair value hierarchy, as these assets have been valued using information obtained through a third-party pricing service at each balance sheet date, using observable market inputs that may include trade information, broker or dealer quotes, bids, offers, or a combination of these data sources.

6. Stock-BASED COMPENSATION

Stock Incentive Plan

General Option Information

A summary of option activity for thenine months ended September 30, 2026 is as follows:

The aggregate intrinsic value of options exercised during the nine months ended September 30, 2026 and 2025 was$16.8 million and$0.9 million, respectively.

The total fair value of stock options vested during the nine months ended September 30, 2026 and 2025 was$10.6 million and$14.6 million, respectively.

Restricted Stock Unit Activity

A summary of restricted stock unit, or RSU, activity for thenine months ended September 30, 2026 is as follows:

Performance-Based Restricted Stock Unit Activity

In 2025, the Company granted performance-based restricted stock units, or PSUs, whereby vesting depends upon the occurrence of certain milestone events, or the 2025 PSUs. When the achievement of milestone events, which include certain clinical milestones related to avexitide for the treatment of PBH, becomes probable, compensation expense will be recognized from the grant date over the requisite service period and a cumulative catch-up adjustment will be recorded to reflect the portion of the employees’ requisite service that has been provided to date. During the three months ended September 30, 2026, the Company recognized$1.7 million of stock-based compensation expense related to a performance condition that was achieved during the period. None of the remaining performance conditions had been deemed probable of being achieved and therefore no additional expense was recognized during the period.

A summary of PSU activity for thenine months ended September 30, 2026, is as follows:

Summary of Stock-Based Compensation Expense

Stock-based compensation expense for thethree and nine months ended September 30, 2026 and 2025, is as follows (in thousands):

The following table summarizes unrecognized stock-based compensation expense as of September 30, 2026, by type of awards (in thousands), and the weighted-average period over which that expense is expected to be recognized (in years). The total unrecognized stock-based compensation expense will be adjusted for actual forfeitures as they occur.

7. STOCKHOLDERS’ EQUITY

Common Stock

Under the Company’s Fourth Amended and Restated Certificate of Incorporation, or the certificate of incorporation, each share of common stock entitles the holder to one vote on all matters submitted to the stockholders for a vote provided, however, that, except as otherwise required by law, holders of common stock shall not be entitled to vote on any amendment to the Company’s certificate of incorporation that relates solely to the terms of one or more outstanding series of preferred stock if the holders of such affected series are entitled, either separately or together with the holders of one or more other such series, to vote thereon pursuant to the certificate of incorporation or pursuant to the Delaware General Corporation Law. Holders of common stock are entitled to receive dividends, as may be declared by the Company’s Board of Directors, if any, subject to the preferential dividend rights of the preferred stock. No dividends were declared or paid during thenine months ended September 30, 2026 and 2025.

Offering

On August 19, 2026, the Company entered into an underwriting agreement with Leerink Partners LLC, Morgan Stanley & Co. LLC, Guggenheim Securities, LLC and LifeSci Capital LLC, as representatives of the several underwriters named therein, relating to the issuance and sale of an aggregate of 16,203,500 shares of the Company’s common stock at a price to the public of$35.50 per share, including the exercise in full by the underwriters of their option to purchase an additional 2,113,500 shares of common stock, or the Offering. The net proceeds from the Offering were approximately$544.6 million, after deducting underwriting discounts and commissions and offering expenses.

8. NET LOSS PER SHARE

Net Loss per Share

Basic earnings per share is computed by dividing net loss by the weighted average number of common shares outstanding during the period. Diluted earnings per share is calculated based on the combined weighted average number of common shares and potentially dilutive shares, which include the assumed exercise of employee stock options, unvested RSUs and unvested PSUs. In computing diluted earnings per share, the Company utilizes the treasury stock method.

Because the Company reports a net loss, basic and diluted net loss per share are the same for both periods presented.

All stock options, RSUs and PSUs units were excluded from the computation of diluted weighted-average shares outstanding because such securities would have an antidilutive impact for the three and nine months ended September 30, 2026. The following stock options, RSUs and PSUs outstanding at each period end have been excluded from the calculation of diluted net loss per share because their inclusion would have been antidilutive:

9. Commitments and Contingencies

Letter of Credit

Restricted cash equivalents consist of$0.9 million of cash serving as collateral for a letter of credit issued for the Company’s office spaces, and$0.1 million as collateral for a corporate credit card program. As of September 30, 2026 and December 31, 2025, the Company’s restricted cash equivalents balance was$1.0 million on its condensed consolidated balance sheets.

Legal Proceedings

On February 9, 2024, a putative class action lawsuit was filed in the U.S. District Court for the Southern District of New York against us and certain of our current and former officers (Shih v. Amylyx Pharmaceuticals, Inc., et al., Case Number 1:24-CV-00988, or the Shih Complaint). Plaintiff filed an amended complaint on June 24, 2024. The Shih Complaint asserted a claim against all defendants for alleged violations of Section 10(b) of the Exchange Act and Rule 10b-5 promulgated thereunder and a claim under Section 20(a) against certain current and former officers as alleged controlling persons. The Shih Complaint alleged that defendants made materially false and misleading statements related to the commercial results and prospects for RELYVRIO. The Shih Complaint sought unspecified damages, interest, costs and attorneys’ fees, and other unspecified relief that the court deems appropriate. On August 12, 2024, the case was transferred from the U.S. District Court for the Southern District of New York to the U.S. District Court for the District of Massachusetts, or the Court, and assigned docket number 1:24-CV-12068. Following the transfer, on September 6, 2024, defendants moved to dismiss the Shih Complaint. On September 30, 2025, the Court issued an order finding that the majority of the alleged misstatements were inactionable, but ultimately denied the motion to dismiss. The Company filed an answer on October 30, 2025. The parties reached an agreement to settle the class claims, subject to court approval, for $6.5 million, a significant portion of which was funded by insurance proceeds. On September 10, 2026, the Court entered a final order and judgment approving the settlement and dismissing the lawsuit with prejudice as to all defendants.

In addition to the Shih Complaint, two derivative complaints were filed in the U.S. District Court for the District of Massachusetts on October 2, 2024, Jones v. Cohen, et al., 1:24-cv-12527, and on July 2, 2025, Hassine v. Cohen, et al., 1:25-CV-11879 (together, the Massachusetts Derivative Complaints) against certain current and former director and officer defendants (and naming the company as a nominal defendant). The substantive allegations in the Massachusetts Derivative Complaints mirror those of the Shih Complaint but assert claims for alleged violations of the Exchange Act, breach of fiduciary duty, insider trading, and unjust enrichment (among other common law claims) and seek unspecified damages to be awarded to the Company along with interest, restitution, unspecified corporate governance and internal procedural reforms and improvements, and plaintiff's attorneys' fees and costs.

On July 16, 2025, the parties to both Massachusetts Derivative Complaints moved the Court to consolidate the two actions and stay the consolidated action, which the Court approved on July 22, 2025. On June 12, 2026, following the lifting of the stay, plaintiffs filed an amended complaint. On July 14, 2026, the parties filed a stipulation with the Court informing it that they were engaged in the negotiation of as settlement term sheet and seeking an extension to existing deadlines to allow the parties to finalize the term sheet and negotiate a formal settlement agreement, which the court granted on July 15, 2026. On August 13, 2026, the parties filed a stipulation with the Court, informing it that they had executed a settlement term sheet and were working to finalize a settlement agreement. The parties’ stipulation requested adjournment of the defendants’ deadline to respond to the complaint and agreed to submit a joint status report on September 14, 2026, which the Court granted on August 14, 2026. The parties have since submitted joint status reports to the Court on September 14 and October 16, 2026, stating that they are continuing to negotiate a settlement agreement and will file a joint status report with the Court on November 16, 2026, if the Plaintiffs have not moved for preliminary approval of the settlement by that date.

On April 7, 2026, a third derivative complaint was filed in Delaware Court of Chancery against certain current and former directors and officer defendants, naming the Company as nominal defendant, Schweitzer v. Klee, et al., 2026-0459-BWD (the Schweitzer Complaint and, together with the Massachusetts Derivative Complaints, the Derivative Complaints). Like the Massachusetts Complaints, the substantive allegations of the Schweitzer Complaint mirror those of the Shih Complaint and allege breach of fiduciary duty and other common law claims and seeks unspecified damages with interest, costs, and attorneys’ fees, restitution, and certain corporate governance and internal procedural reforms and improvements. The Schweitzer Complaint plaintiff is participating in the above-referenced settlement negotiations to attempt to resolve the Derivative Complaints, and the case is currently stayed by a court order dated August 20, 2026. To the extent a resolution of the Derivative Complaints cannot be reached, we intend to defend against the Derivative Complaints vigorously. At this time, an estimate of the impact, if any, of the claims made in the Derivative Complaints cannot be made.

Royalty Payments

The Company has entered into a limited number of grant and royalty agreements that include payment obligations contingent upon future events, such as commercialization or the receipt of proceeds from revenue-generating transactions related to the underlying technologies. As the conditions that would trigger royalty payments have not been met, no amounts have been recorded in the consolidated financial statements.

Purchase Commitments

The Company enters into agreements in the normal course of business with contract manufacturing organizations, or CMOs, for raw material purchases and manufacturing services. As of September 30, 2026, the Company had approximately$30.0 million of remaining unconditional purchase obligations that are expected to be paid through 2028. Of this amount, approximately$18.8 million is expected to be paid within the next 12 months, and approximately$11.3 million is expected to be paid thereafter through 2028.

10. asset aCQUISITIONS and collaboration agreements

Gubra A/S Collaboration and License Agreement

In December 2024, the Company entered into a collaboration and license agreement, or the Gubra Agreement, with Gubra A/S, or Gubra, pursuant to which the parties will perform research and discovery activities for the development of a potential novel long-acting GLP-1 receptor antagonist, under the oversight of a joint research committee. The collaboration provides the Company with an exclusive license to develop, manufacture, commercialize and otherwise exploit any development candidate and product(s) arising in the performance of activities under the agreement.

The Company made an immaterial upfront payment in January 2025, which became due upon the effective date of the Gubra Agreement. Given the payment was made for the use of Gubra’s intellectual property and research and development services and there is no alternative use, the Company recorded the upfront payment to research and development expense on the consolidated statements of operations in 2024. Certain milestones were met and paid in the first quarter of 2026, specifically the selection and handover of the development candidate, which provided a milestone payment of $4.0 million to Gubra. Gubra is eligible to receive an additional$49.5 million upon the achievement of certain development, regulatory and commercial milestones, as well as tiered royalties on future sales from any products that result from the First Gubra Agreement. None of these milestone payments are deemed probable at September 30, 2026 and have not been recognized.

In July 2026, the Company entered into a second collaboration and license agreement, or the Second Gubra Agreement, with Gubra, pursuant to which the parties will perform research and discovery activities to identify potential development candidates for a rare endocrine disease, under the oversight of a joint steering committee. The collaboration provides the Company an exclusive license to develop, manufacture, commercialize and otherwise exploit any development candidate and product(s) arising in the performance of activities under the Second Gubra Agreement.

The Company made an immaterial upfront payment in August 2026, which became due upon the effective date of the Second Gubra Agreement. Given the payment was made for the use of Gubra’s intellectual property and research and development services and there is no alternative use, the Company recorded the upfront payment to research and development expense on the consolidated statements of operations during the current period. Gubra is eligible to receive additional payments upon the achievement of certain development, regulatory and commercial milestones, as well as tiered royalties on future sales from any products that result from the agreement. None of these milestone payments are deemed probable at September 30, 2026 and have not been recognized. The Company has also agreed to make quarterly payments to fund Gubra’s ongoing research activities, which are not expected to be material.

11. Segments

The Company views its operations and manages its business asone operating segment and reporting unit. Our operating segments are determined based on how our Co-Chief Executive Officers, who collectively serve as our chief operating decision makers, or CODM, manage our business, regularly access discrete financial information, and evaluate performance for operating decision-making purposes, including allocation of resources or capital to specific compounds or projects in line with the Company’s overall strategies and goals. The Company’s entire business is managed by a single management team, which reports to the CODM.

The CODM assess segment performance and decide how to allocate resources based on consolidated net loss. The CODM use net loss to monitor budget and forecast versus actual results in assessing segment performance and to determine how to allocate resources. The measure of segment assets used in determining how to manage and allocate resources is reported on the consolidated balance sheets as total assets. All of the Company's long-lived assets were held within the U.S.

The following table reconciles segment revenue and expenses to consolidated net loss for thethree and nine months ended September 30, 2026 and 2025 (in thousands):

1. The significant expense categories and amounts align with the segment-level information that is regularly provided to the CODM. As the Company hasone reportable segment, there wereno intersegment eliminations for thethree and nine months ended September 30, 2026 and 2025.

2. Depreciation and amortization expenseof less than 0.1 million and$0.2 million during the three and nine months ended September 30, 2026, respectively, and$0.1 million and$0.4 million during the three and nine months ended September 30, 2025, respectively, are allocated across the significant expense captions.

3. Other programs includes milestone payments totaling $4.0 million made to Gubra following the selection and handover of AMX0318 as a development candidate for PBH and other rare diseases during thenine months ended September 30, 2026.

4. The Company does not allocate personnel and other similar costs to specific programs because these costs are deployed across multiple programs.

5. Other segment items primarily consists of net realized and unrealized losses on foreign exchange transactions.