Material Agreement Form 8 K

On January 10, 2025, Amylyx Pharmaceuticals, Inc. ("Amylyx" or the "Company") entered into an underwriting agreement (the "Underwriting Agreement") with Leerink Partners LLC, as representative of the several underwriters named therein (the "Underwriter"), relating to the issuance and sale of an aggregate of 17,142,857 shares (the "Firm Shares") of the Company's common stock, par value $0.0001 per share ("Common Stock"), at a price to the public of $3.50 per share (the "Offering"). Pursuant to the Underwriting Agreement, the Company also granted the Underwriter a 30-dayoption to purchase up to 2,571,428 additional shares of Common Stock at the public offering price less the underwriting discounts and commissions (the "Option Shares" and together with the Firm Shares, the "Shares").

The aggregate net proceeds to the Company, after deducting underwriting discounts and commissions and other estimated offering expenses payable by the Company, will be approximately $56.9 million, or approximately $65.5 million if the option to purchase the Option Shares is exercised in full by the Underwriter. Amylyx intends to use the net proceeds from this offering, together with existing cash, cash equivalents and marketable securities, to advance preparations for commercialization and pipeline programs, for working capital and for general corporate purposes. The Offering is expected to close on January 13, 2025, subject to customary closing conditions. All of the Shares in the Offering are being sold by the Company.

The Underwriting Agreement contains customary representations and warranties, conditions to closing, market standoff provisions, termination provisions and indemnification obligations, including for liabilities under the Securities Act of 1933, as amended. The representations, warranties and covenants contained in the Underwriting Agreement were made only for purposes of such agreement and as of specific dates, and were solely for the benefit of the parties to the Underwriting Agreement.

The Offering is being made pursuant to a prospectus supplement, dated January 10, 2025 (the "Prospectus Supplement"), filed with the Securities and Exchange Commission ("SEC") on January 10, 2025 and an accompanying base prospectus that forms a part of the registration statement on Form S-3ASR(File No. 333-270505), filed with the SEC on March 13, 2023, which was effective upon filing with the SEC. This Current Report on Form 8-Kdoes not constitute an offer to sell or a solicitation of an offer to buy shares of Common Stock.

The foregoing description of certain terms of the Underwriting Agreement and the transactions contemplated thereby does not purport to be complete and is subject to and qualified in its entirety by reference to the full text of the Underwriting Agreement that is filed as Exhibit 1.1 to this Current Report on Form 8-Kand is incorporated by reference herein.

The legal opinion of Goodwin Procter LLP relating to the legality of the issuance and sale of the Shares in the Offering is filed as Exhibit 5.1 to this Current Report on Form 8-K.

Forward Looking Statements

Statements contained in this Current Report on Form 8-Kregarding matters that are not historical facts are "forward-looking statements" within the meaning of the Private Securities Litigation Reform Act of 1995, as amended, including with respect to the completion of the proposed Offering, the anticipated closing date of the Offering, the expected amount of proceeds from the Offering and the expected use of proceeds from the offering. No assurance can be given that the Offering discussed above will be completed. Because such statements are subject to risks and uncertainties, actual results may differ materially from those expressed or implied by such forward-looking statements. Any forward-looking statements in this Current Report on Form 8-Kare based on management's current expectations of future events and are subject to a number of risks and uncertainties that could cause actual results to differ materially and adversely from those set forth in or implied by such forward-looking statements. Risks that contribute to the uncertain nature of the forward-looking statements include those risks and uncertainties set forth in Amylyx' SEC filings, including Amylyx' Annual Report on Form 10-Kfor the year ended December 31, 2023, Quarterly Report on Form 10-Qfor the quarterly period ended September 30, 2024, and subsequent filings with the SEC. All forward-looking statements contained in this Current Report on Form 8-Kspeak only as of the date on which they were made. Amylyx undertakes no obligation to update such statements to reflect events that occur or circumstances that exist after the date on which they were made. In light of the foregoing, investors are urged not to rely on any forward-looking statement in reaching any conclusion or making any investment decision about any securities of Amylyx.