UNITED STATES

SECURITIES AND EXCHANGE COMMISSION

WASHINGTON, D.C. 20549

FORM 8-K

CURRENT REPORT

Pursuant to Section 13 or 15(d)

of the Securities Exchange Act of 1934

Date of Report (Date of earliest event reported): May 25, 2017 (May 23, 2017)

Alnylam Pharmaceuticals, Inc.

(Exact Name of Registrant as Specified in Charter)

Registrant’s telephone number, including area code: (617) 551-8200

Not applicable

(Former Name or Former Address, if Changed Since Last Report)

Check the appropriate box below if the Form 8-K filing is intended to simultaneously satisfy the filing obligation of the registrant under any of the following provisions (see General Instruction A.2. below):

Indicate by check mark whether the registrant is an emerging growth company as defined in Rule 405 of the Securities Act of 1933 (§230.405 of this chapter) or Rule 12b-2 of the Securities Exchange Act of 1934(§240.12b-2 of this chapter).

Emerging growth company  ☐

If an emerging growth company, indicate by check mark if the registrant has elected not to use the extended transition period for complying with any new or revised financial accounting standards provided pursuant to Section 13(a) of the Exchange Act.  ☐

On May 23, 2017, Alnylam Pharmaceuticals, Inc. (the “Company”) entered into an underwriting agreement (the “Underwriting Agreement”) with Barclays Capital Inc. (the “Underwriter”), relating to an underwritten public offering of 5,000,000 shares (the “Shares”) of the Company’s common stock, par value $0.01 per share (the “Common Stock”). All of the shares are being sold by the Company. The offering price to the public is $71.87 per share, and the Underwriter has agreed to purchase the Shares from the Company pursuant to the Underwriting Agreement at a price of $71.13 per share. After underwriting discounts and commissions and estimated offering expenses, the Company expects to receive net proceeds from the offering of approximately $355.2 million (assuming the Underwriter does not exercise its option to purchase additional shares referenced below). Under the terms of the Underwriting Agreement, the Company granted the Underwriter an option, exercisable for 30 days, to purchase up to an additional 750,000 shares of Common Stock at the same price per share as the Shares solely to cover over-allotments.

The Shares will be issued pursuant to an automatically effective shelf registration statement that the Company filed with the Securities and Exchange Commission (the “SEC”) on May 5, 2017 (File No. 333-217688). A prospectus supplement relating to the offering has been filed with the SEC. The offering is expected to close on May 30, 2017, subject to the satisfaction of customary closing conditions.

A copy of the Underwriting Agreement is attached as Exhibit 1.1 hereto and is incorporated herein by reference. The foregoing description of the material terms of the Underwriting Agreement does not purport to be complete and is qualified in its entirety by reference to such exhibit.

A copy of the legal opinion and consent of Goodwin Procter LLP relating to the Shares is attached as Exhibit 5.1 hereto.

Pursuant to the Investor Agreement dated February 27, 2014 by and between the Company and Genzyme Corporation (“Sanofi Genzyme”), Sanofi Genzyme has the right, subject to certain exceptions, generally to maintain its ownership percentage in the Company until Sanofi Genzyme owns less than 7.5% of the Company’s outstanding common stock, including a right to purchase shares in connection with public offerings by the Company (the “Offering Right”).

On May 24, 2017, in connection with the offering described under Item 1.01, Sanofi Genzyme notified the Company of its intent to exercise the Offering Right and purchase directly from the Company in a private placement 297,501 shares of the Company’s common stock at a price of $71.87 per share, the public offering price, for aggregate proceeds of approximately $21.4 million. The private placement is expected to be completed on May 30, 2017, subject to the closing of the offering.

The shares of common stock to be issued to Sanofi Genzyme pursuant to the Offering Right will be issued pursuant to the exemption from registration set forth in Section 4(a)(2) of the Securities Act of 1933, as amended, as the issuance does not involve a public offering.

A copy of the press release announcing the pricing of the public offering is attached to this Current Report on Form 8-K as Exhibit 99.1.

(d) Exhibits

SIGNATURE

Pursuant to the requirements of the Securities Exchange Act of 1934, the registrant has duly caused this report to be signed on its behalf by the undersigned hereunto duly authorized.

EXHIBIT INDEX