UNITED STATES

SECURITIES AND EXCHANGE COMMISSION

WASHINGTON, DC 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): November 9, 2012

Idera Pharmaceuticals, Inc.

(Exact Name of Registrant as Specified in Charter)

Registrant’s telephone number, including area code: (617) 679-5500

(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):

Item 1.01. Entry Into a Material Definitive Agreement.

Convertible Preferred Stock and Warrant Purchase Agreement

On November 9, 2012, Idera Pharmaceuticals, Inc. (“Idera” or “the Company”) entered into a Convertible Preferred Stock and Warrant Purchase Agreement (the “Series E Purchase Agreement”) with Pillar Pharmaceuticals II, L.P. (“Pillar II”), an investment partnership, and the other purchaser named therein (together with Pillar II, the “Purchasers”). Youssef El Zein is a member of the Company’s board of directors (the “Board”), and is a director and controlling stockholder of the general partner of Pillar II. Pursuant to the Series E Purchase Agreement, the Company issued and sold to the Purchasers, for an aggregate purchase price of $6,999,993, 424,242 shares of its Series E convertible preferred stock, par value $0.01 per share (“Series E Preferred Stock”), convertible into 8,484,840 shares of common stock, $0.001 par value per share, of the Company (“Common Stock”), and warrants (the “Warrants”) to purchase 8,484,840 shares of Common Stock. Each share of Series E Preferred Stock is convertible into 20 shares of Common Stock at a conversion price of $0.70 per share.

Under the terms of the Series E Purchase Agreement, the Company granted the Purchasers participation rights in future financings. In addition, the Company agreed to use its best efforts to file a preliminary proxy statement for its next annual meeting of stockholders that will, among other things, seek approval from the Company’s stockholders in accordance with Section 5.11 of the Series E Purchase Agreement of the following matters:

Also under the terms of the Series E Purchase Agreement, each Purchaser agreed:

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The Warrants have an exercise price of $0.70 per share (subject to adjustment) and may be exercised at the Purchaser’s option at any time on or before November 9, 2017. The Warrants provide that the Company may not effect any exercise of the Warrants, and the Warrants may not be exercised with respect to any portion of the Warrants, to the extent that such exercise would result in the Purchaser and its affiliates beneficially owning more than 19.99% of the outstanding Common Stock or outstanding voting power of the Company (including shares of Common Stock issuable upon conversion of the Series E Preferred Stock and exercise of the Warrants), unless the stockholders of the Company approve the Nasdaq Proposal, in which case, the 19.99% limitation will be increased, with respect to any holder of Series E Preferred Stock, to 35%. The Warrants also provide that at any time after November 9, 2014 the Company may redeem the Warrants for $0.01 per share of Common Stock issuable on exercise of the Warrants following notice to the Purchaser if the closing price of the Common Stock for 20 or more trading days in a period of 30 consecutive trading days is greater than or equal to $2.80 (subject to adjustment); provided, however, that the Company may not redeem any Warrants from a holder that cannot exercise such Warrants as a result of the beneficial ownership limitations on exercise described above.

The Series E Purchase Agreement is attached hereto as Exhibit 10.1 and is incorporated herein by reference. The form of Warrant to be issued to the Purchasers is attached hereto as Exhibit 10.3 and is incorporated herein by reference. The foregoing descriptions of the Series E Purchase Agreement and the Warrants do not purport to be complete and are qualified in their entirety by reference to such exhibits.

Registration Rights Agreement

In connection with the Series E Purchase Agreement, the Company entered into a Registration Rights Agreement, dated November 9, 2012, with the Purchaser (the “Registration Rights Agreement”). Pursuant to the Registration Rights Agreement, the Company has agreed to file a registration statement with the Securities and Exchange Commission registering the resale of the shares of Common Stock issuable upon conversion of the Series E Preferred Stock and the shares of Common Stock issuable upon exercise of the Warrants. The Company is subject to specified cash penalties if it fails to file and maintain an effective registration statement. Such penalties are limited to a cumulative maximum penalty equal to 10% of the gross proceeds from the sale of the Series E Preferred Stock. The Company is required to use its reasonable best efforts to maintain the registration statement’s effectiveness until no shares of Common Stock issued or issuable upon conversion of the Series E Preferred Stock or upon exercise of the Warrants remain outstanding or issuable, as applicable.

The Registration Rights Agreement is attached hereto as Exhibit 10.2 and is incorporated herein by reference. The foregoing description of the Registration Rights Agreement does not purport to be complete and is qualified in its entirety by reference to such exhibit.

Amendment to Series D Purchase Agreement

On November 9, 2012, the Company entered into Amendment No. 1 (“Amendment No. 1 to Series D Purchase Agreement”) to the Convertible Preferred Stock and Warrant Purchase Agreement, dated as of November 4, 2011 (the “Series D Purchase Agreement”), between the Company and Pillar I. Mr. El Zein is a director and controlling stockholder of the general partner of Pillar I. Pursuant to Amendment No. 1 to Series D Purchase Agreement, the provisions set forth in the Series D Purchase Agreement related to the voting of certain excess shares held by Pillar I and the transfer restrictions imposed on securities purchased by Pillar I thereunder were amended to provide:

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Amendment No. 1 to Series D Purchase Agreement is attached hereto as Exhibit 10.4 and is incorporated herein by reference. The foregoing description of Amendment No. 1 to Series D Purchase Agreement does not purport to be complete and is qualified in its entirety by reference to such Exhibit.

Amendment to Series D Warrant

On November 9, 2012, the Company entered into Amendment No. 1 (“Amendment No. 1 to Series D Warrant”) to the Warrant to Purchase Common Stock, dated as of November 4, 2011 (the “Series D Common Stock Warrant”), issued by the Company to Pillar I pursuant to the Series D Purchase Agreement. Pursuant to Amendment No. 1 to Series D Warrant, the provisions set forth in the Series D Common Stock Warrant limiting the Company’s redemption rights with respect to the warrants issued pursuant to the Series D Purchase Agreement were amended to provide that the Company may not effect any exercise of such warrants, and such warrants may not be exercised with respect to any portion of such warrants, to the extent that such exercise would result in Pillar I and its affiliates beneficially owning more than 19.99% of the outstanding Common Stock or outstanding voting power of the Company (including shares of Common Stock issuable upon conversion of the Series D Preferred Stock and exercise of such warrants), unless the stockholders of the Company approve the Nasdaq Proposal, in which case, the 19.99% limitation will be increased, with respect to Pillar I, to 35%.

Amendment No. 1 to Series D Warrant is attached hereto as Exhibit 10.5 and is incorporated herein by reference. The foregoing description of Amendment No. 1 to Series D Warrant does not purport to be complete and is qualified in its entirety by reference to such Exhibit.

Item 3.02. Unregistered Sales of Equities Securities.

Pursuant to the Purchase Agreement, on November 9, 2012, the Company issued and sold to the Purchasers, for an aggregate purchase price of $6,999,993, 424,242 shares of its Series E Preferred Stock, convertible into 8,484,840 shares of Common Stock, and Warrants to purchase 8,484,840 shares of Common Stock at a per share exercise price of $0.70 (subject to adjustment). Each share of Series E Preferred Stock is convertible into 20 shares of Common Stock at a per share conversion price of $0.70 (subject to adjustment).

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The shares of Series E Preferred Stock and Warrants offered and sold pursuant to the Series E Purchase Agreement were offered and sold to the Purchasers without registration under the Securities Act of 1933, as amended (the “Securities Act”) or the securities laws of certain states, in reliance on the exemption provided by Regulation S under the Securities Act.

Item 3.03. Material Modification to Rights of Security Holders.

Pursuant to Section 4.4.4 of the Series D Certificate of Designations, the conversion price for the Series D Preferred Stock, which was initially set at $1.6275, is required to be adjusted if, among other things, at any time after the original issue date of the Series D Preferred Stock issues Additional Shares of Common Stock (as defined in the Series D Certificate of Designations) without consideration or for consideration per share less than $1.46 (subject to adjustment); provided, however, that the conversion price may not be adjusted to a price that is less than $1.46 (subject to adjustment). As a result of the issuance of the Series E Preferred Stock and Warrants in the transactions described under Item 1.01 of this Current Report, the conversion price of the Series D Preferred Stock has been adjusted to $1.46 pursuant to the terms of the Series D Certificate of Designations. Pursuant to Section 4.9 of the Series D Certificate of Designations, the Company will mail to each holder of Series D Preferred Stock a certificate notifying the holders of the new conversion price.

Pursuant to Section 2(a) of the Series D Common Stock Warrant, in the event the conversion price for the Series D Preferred Stock is adjustment pursuant to the Series D Certificate of Designations, the exercise price with respect to the shares of Common Stock issuable upon exercise of the Series D Common Stock Warrant is required to be adjusted, concurrently with the adjustment to the Series D Preferred Stock conversion price, in the same manner and in the same proportion as the Series D Preferred Stock conversion price is so adjusted. As a result of the issuance of the Series E Preferred Stock and the Warrants in the transactions described under Item 1.01 of this Current Report, the exercise price with respect to the shares of Common Stock issuable upon exercise of the Series D Common Stock Warrant has been adjusted to $1.46 pursuant to the terms of the Series D Common Stock Warrant. Pursuant to Section 2(f) of the Series D Common Stock Warrant, the Company will mail to each holder of a Series D Common Stock Warrant a certificate notifying the holders of the new exercise price.

Item 5.02. Departure of Directors or Certain Officers; Election of Directors; Appointment of Certain Officers; Compensatory Arrangements of Certain Officers

On November 9, 2012, the Board elected Abdul-Wahab Umari to the Board as a Class I director. Mr. Umari’s term as a Class I director will expire at the Company’s 2014 annual meeting of stockholders.

In accordance with the Company’s director compensation program, Mr. Umari will receive an annual cash retainer of $35,000 for service on the Board, which is payable quarterly in arrears. The Company’s director compensation program includes a stock-for-fees policy, under which Mr. Umari has the right to elect, on a quarterly basis, to receive Common Stock of the Company in lieu of the cash fees. Mr. Umari has not elected to receive the Company’s Common Stock for fees at this time.

In addition, under the Company’s director compensation program, upon his election to the Board, Mr. Umari was granted an option to purchase 30,000 shares of the Company’s Common Stock at an exercise price of $0.69 per share. Pursuant to the Company’s director compensation program, Mr. Umari will also receive an annual option grant to purchase 20,000 shares of the Company’s Common Stock on the date of the Company’s annual meeting of stockholders. All options granted to non-employee directors have an exercise price equal to the closing price of the Company’s Common Stock on the date of grant and vest in equal quarterly installments over three years, subject to continued service as a director. These options automatically become exercisable in full upon the occurrence of a change in control of the Company.

Mr. Umari will be subject to the Company’s Director Retirement Policy, which provides for acceleration of vesting of options and an extension of the exercise period upon the retirement of a non-employee director, as more fully described in the Company’s Proxy Statement filed on April 27, 2012 with the Securities and Exchange Commission.

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Mr. Umari was elected by the Board upon the recommendation of the Nominating and Corporate Governance Committee. Mr. Umari was elected to the Board in connection with the closing of the purchase by Pillar II of the Company’s securities in the transactions described under Item 1.01 of this Current Report.

Mr. Umari is a managing partner of the general partner of Pillar I and Pillar II. The Company believes that the terms of its transactions with Pillar I and Pillar II, as described under Item 1.01 of this Current Report, were no less favorable than those that the Company could have obtained from unaffiliated third parties.

Item 5.03. Amendments to Articles of Incorporation or Bylaws; Change in Fiscal Year.

The Certificate of Incorporation permits the Board to issue up to 5,000,000 shares of preferred stock, par value $0.01 per share, in one or more series, to designate the number of shares constituting such series, and fix by resolution, the powers, privileges, preferences and relative, optional or special rights thereof, including liquidation preferences and dividends, and conversion and redemption rights of each such series. On November 9, 2012, the Board of the Company designated 424,242 shares as Series E Preferred Stock, having the rights and preferences set forth in the Certificate of Designations as summarized below.

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The Certificate of Designations is attached hereto as Exhibit 3.1 and incorporated herein by reference. The description of the Certificate of Designations does not purport to be complete and is qualified in its entirety by reference to such Exhibit.

Item 9.01. Financial Statements and Exhibits.

See Exhibit Index attached hereto.

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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.

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EXHIBIT INDEX

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