UNITED STATES

SECURITIES AND EXCHANGE COMMISSION

Washington, DC 20549

FORM 10-Q/A

Amendment No. 1

(Mark One)

☒QUARTERLY REPORT PURSUANT TO SECTION 13 OR 15(d) OF THE SECURITIES EXCHANGE ACT OF 1934

For the quarterly period ended March 31, 2016

OR

◻TRANSITION REPORT PURSUANT TO SECTION 13 OR 15(d) OF THE SECURITIES EXCHANGE ACT OF 1934

Commission file number 001-37359

BLUEPRINT MEDICINES CORPORATION

(Exact Name of Registrant as Specified in Its Charter)

(617) 374-7580

(Registrant’s Telephone Number, Including Area Code)

(Former Name, Former Address and Former Fiscal Year, if Changed Since Last Report)

Indicate by check mark whether the registrant: (1) has filed all reports required to be filed by Section 13 or 15(d) of the Securities Exchange Act of 1934 during the preceding 12 months (or for such shorter period that the registrant was required to file such reports), and (2) has been subject to such filing requirements for the past 90 days.    Yes  ☒     No  ◻

Indicate by check mark whether the registrant has submitted electronically and posted on its corporate Web site, if any, every Interactive Data File required to be submitted and posted pursuant to Rule 405 of Regulation S-T (§232.405 of this chapter) during the preceding 12 months (or for such shorter period that the registrant was required to submit and post such files).    Yes  ☒     No  ◻

Indicate by check mark whether the registrant is a large accelerated filer, an accelerated filer, a non-accelerated filer, or a smaller reporting company. See the definitions of “large accelerated filer,” “accelerated filer” and “smaller reporting company” in Rule 12b-2 of the Exchange Act. (Check one):

Indicate by check mark whether the registrant is a shell company (as defined in Rule 12b-2 of the Exchange Act).    Yes  ◻     No  ☒

Number of shares of the registrant’s common stock, $0.001 par value, outstanding on May 6, 2016: 27,238,661

Explanatory Note

Blueprint Medicines Corporation (the “Company”) is filing this Amendment No. 1 on Form 10-Q/A (this “Amendment No. 1”) to amend its Quarterly Report on Form 10-Q for the quarterly period ended March 31, 2016, as filed with the Securities and Exchange Commission (“SEC”) on May 10, 2016 (the “Quarterly Report”). This Amendment No. 1 is being filed solely to file revised redacted versions of Exhibits 10.1 and 10.2 (the “Exhibits”), which were previously filed with the Quarterly Report, in response to comments from the SEC regarding a confidential treatment request submitted to the SEC with respect to the Exhibits. The revised Exhibits attached to this Amendment No. 1 as Exhibit 10.1 and Exhibit 10.2, respectively, supersede and replace the versions of the Exhibits previously filed with the Quarterly Report. Certain portions of the information that was omitted from the Exhibits previously filed with the Quarterly Report have now been included as part of the revised Exhibits.

Except for the revised Exhibits, this Amendment No. 1 does not amend any information set forth in the Quarterly Report. This Amendment No. 1 speaks as of the original filing date of the Quarterly Report and does not reflect any events that occurred at a date subsequent to the filing of the Quarterly Report or modify or update those disclosures therein in any way. Accordingly, this Amendment No. 1 should be read in conjunction with the Company’s Quarterly Report and any filings made with the SEC subsequent to the filing of the Quarterly Report. As required by Rule 12b-15 under the Securities Exchange Act of 1934, as amended, the Company is filing new certifications by its principal executive officer and principal financial officer pursuant to Section 302 of the Sarbanes-Oxley Act of 2002 as exhibits to this Amendment No. 1.

SIGNATURES

Pursuant to the requirements of Section 13 or 15(d) of the Securities Exchange Act of 1934, the registrant has duly caused this report to be signed on its behalf by the undersigned, thereunto duly authorized.

EXHIBIT INDEX