UNITED STATES

SECURITIES AND EXCHANGE COMMISSION

WASHINGTON, D.C. 20549

SCHEDULE TO

TENDER OFFER STATEMENT UNDER SECTION 14(d)(1) OR SECTION 13(e)(1)

OF THE SECURITIES EXCHANGE ACT OF 1934

(Amendment No. 2)

CUBIST PHARMACEUTICALS, INC.

(Name of Subject Company (Issuer))

CUBIST PHARMACEUTICALS, INC.

(Name of Filing Persons (Issuer))

2.50% Convertible Senior Notes due 2017

1.125% Convertible Senior Notes due 2018

1.875% Convertible Senior Notes due 2020

(Title of Class of Securities)

229678 AD9

229678 AF4

229678 AH0

(CUSIP Number of Class of Securities)

Sunil A. Patel

2000 Galloping Hill Road

K1-3045

Kenilworth, NJ 07033

(908) 740-4000

(Name, address and telephone number of person authorized to receive notices and communications on behalf of filing persons)

with copies to:

Andrew F. Fowler

David Schwartz

Hughes Hubbard & Reed LLP

One Battery Park Plaza

New York, NY 10004

Phone: (212) 837-6000

CALCULATION OF FILING FEE

Check the appropriate boxes to designate any transactions to which the statement relates:

Check the following box if the filing is a final amendment reporting the results of the tender offer:  x

INTRODUCTORY STATEMENT

This Amendment No. 2 amends and supplements the Tender Offer Statement on Schedule TO-I filed with the Securities and Exchange Commission (as amended and supplemented from time to time, the “Schedule TO”) by Cubist Pharmaceuticals, Inc. (the “Company”) with respect to the right of each holder (each, a “Holder”) of (i) the Company’s 2.50% Convertible Senior Notes due 2017 (the “2017 Convertible Notes”), (ii) the Company’s 1.125% Convertible Senior Notes due 2018 (the “2018 Convertible Notes”), and (iii) the Company’s 1.875% Convertible Senior Notes due 2020 (the “2020 Convertible Notes” and together with the 2017 Convertible Notes and 2018 Convertible Notes, the “Notes”), to require the Company to repurchase, at the Holder’s option, 100% of the principal amount of the Notes, plus accrued and unpaid interest thereon to, but excluding, February 23, 2015 (unless such Fundamental Change Repurchase Date falls after a Regular Record Date and on or prior to the corresponding Interest Payment date, in which case the Company shall pay the full amount of accrued and unpaid interest payable on such Interest Payment Date to the Holder of record at the close of business on such Regular Record Date), pursuant to the terms and conditions of the Fundamental Change Repurchase Right Notice, Notice of Right to Convert, Notice of Entry into Supplemental Indenture and Offer to Repurchase dated January 22, 2015 filed as Exhibit (a)(1) to the Schedule TO, as amended and supplemented by the Amendment and Supplement dated January 27, 2015 to Fundamental Change Repurchase Right Notice, Notice of Right to Convert, Notice of Entry into Supplemental Indenture and Offer to Repurchase dated January 22, 2015 filed as Exhibit (a)(1)(i) to the Schedule TO (as so amended and supplemented, the “ Notice”).

This Schedule TO was, and this Amendment is, intended to satisfy the disclosure requirements of Rule 13e-4(c)(2) under the Securities Exchange Act of 1934, as amended (the “Exchange Act”).

Items 1 through 9, and Item 11.

Items 1 through 9 and Item 11 of the Schedule TO are hereby amended and supplemented by adding the following text thereto:

In accordance with the terms of the Notice, the Fundamental Change Repurchase Right expired at the end of the day, immediately after 11:59 p.m., Eastern time, on February 19, 2015 (the “Fundamental Change Expiration Time”), and was not extended. The Company has been advised by the Paying Agent, Conversion Agent and Information Agent that none of the Notes were validly surrendered for repurchase prior to the Fundamental Change Expiration Time. A copy of the press release announcing the final results of the tender offer is filed as Exhibit (a)(5)(i) and incorporated by reference herein.

Item 12. Exhibits.

Item 12 of the Schedule TO is hereby amended and supplemented to include the following exhibit:

SIGNATURE

After due inquiry and to the best of my knowledge and belief, I certify that the information set forth in this statement is true, complete and correct.

Date: February 23, 2015

EXHIBIT INDEX