ALNY Alnylam Pharmaceuticals Inc

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): July 14, 2015 (July 14, 2015)

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):

On July 14, 2015, Alnylam Pharmaceuticals, Inc., a Delaware corporation (the “Company”), filed with the Delaware Secretary of State a Certificate of Elimination (the “Certificate of Elimination”), which returned the 125,000 shares of unissued Series A Junior Participating Preferred Stock, par value $.01 per share, that had been designated in 2005 in connection with a stockholder rights plan that expired on July 13, 2015 (the “Rights Plan”), to the status of authorized but unissued shares of the preferred stock of the Company, without designation as to series or rights, preferences, privileges or limitations.

The foregoing summary of the Certificate of Elimination is qualified in its entirety by reference to the full text of the Certificate of Elimination, which is set forth as Exhibit 4.1 to this Current Report on Form 8-K and incorporated herein by reference.

In connection with the expiration of the Rights Plan, the Company will also take routine, voluntary actions to deregister the related preferred stock purchase rights under the Securities Exchange Act of 1934, as amended, and to delist the preferred stock purchase rights from the Nasdaq Global Select Market. These actions are administrative in nature and will have no effect on the Company’s common stock, which continues to be listed on the Nasdaq Global Select Market.

Forward Looking Statements

This Current Report on Form 8-K contains forward-looking statements that are made pursuant to the safe harbor provisions of the Private Securities Litigation Reform Act of 1995. These statements are neither promises nor guarantees, and are subject to a variety of risks and uncertainties, many of which are beyond the control of the Company, which could cause actual results to differ materially from those contemplated in these forward-looking statements. For additional disclosure regarding these and other risks faced by the Company, see the disclosures contained in the Company’s public filings with the Securities and Exchange Commission, including its most recent Quarterly Report on Form 10-Q filed on May 8, 2015.

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

Exhibit 4.1

CERTIFICATE OF ELIMINATION OF THE

SERIES A JUNIOR PARTICIPATING PREFERRED STOCK OF

ALNYLAM PHARMACEUTICALS, INC.

Pursuant to Section 151(g)

of the General Corporation Law

of the State of Delaware

Alnylam Pharmaceuticals, Inc., a Delaware corporation (the “Company”), in accordance with the provisions of Section 151(g) of the General Corporation Law of the State of Delaware, hereby certifies as follows:

1. That, pursuant to Section 151 of the General Corporation Law of the State of Delaware and authority granted in the Amended and Restated Certificate of Incorporation of the Company, as theretofore amended (the “Certificate of Incorporation”), the Board of Directors of the Company, by resolution duly adopted, authorized the issuance of a series of 125,000 shares of Series A Junior Participating Preferred Stock, par value $.01 per share, of the Company (the “Series A Junior Preferred Stock”), and established the voting powers, designations, preferences and relative, participating, optional or other rights, if any, or the qualifications, limitations or restrictions thereof, and, on July 14, 2005, filed a Certificate of Designations (the “Certificate of Designations”) with respect to such Series A Junior Preferred Stock in the office of the Secretary of State of the State of Delaware (the “Secretary of State”).

2. That no shares of said Series A Junior Preferred Stock are outstanding and no shares thereof will be issued subject to said Certificate of Designations.

3. That the Board of Directors of the Company has adopted the following resolutions:

4. That, accordingly, all matters set forth in the Certificate of Designations with respect to the Preferred Stock be, and hereby are, eliminated from the Certificate of Incorporation, as heretofore amended, of the Company.

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IN WITNESS WHEREOF, Alnylam Pharmaceuticals, Inc. has caused this Certificate of Elimination to be duly executed this 14^th day of July, 2015.

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