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): December 13, 2016

BioMarin Pharmaceutical Inc.

(Exact name of Registrant as Specified in Its Charter)

Registrant’s Telephone Number, Including Area Code: (415) 506-6700

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 Instructions A.2. below):

Item 1.01Entry into a Material Definitive Agreement.

On December 13, 2016, the Board of Directors (the “Board”) of BioMarin Pharmaceutical Inc. (“BioMarin” or the “Company”), at the recommendation of the Corporate Governance and Nominating Committee of the Board, approved a new form of indemnification agreement to be entered into with its directors and executive officers (the “Indemnification Agreement”). The Company has entered into, or will be entering into, an Indemnification Agreement with each of its directors and executive officers.

Consistent with the indemnification agreements previously in effect, the Indemnification Agreement provides that BioMarin will indemnify each of the covered directors and executive officers to the fullest extent permitted by law for claims arising in such person’s capacity as a director, executive officer, employee or other agent of BioMarin, provided that, among other things, such director and/or executive officer acted in good faith and with a view to the best interests of BioMarin and, with respect to any criminal proceeding, had no reasonable grounds for believing that his or her conduct was unlawful.

The foregoing description of the Indemnification Agreement does not purport to be complete and is qualified in its entirety by reference to the form Indemnification Agreement, a copy of which is attached hereto as Exhibit 10.1 and incorporated herein by reference.

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

On December 13, 2016, at the recommendation of the Compensation Committee of the Board, the Board approved the amendment and restatement of the employment agreement (the “Restated Employment Agreement”) of Jean-Jacques Bienaimé, the Company’s Chief Executive Officer and Chair of the Board (the “CEO”). The Company and the CEO entered into the Restated Employment Agreement, effective December 13, 2016. The Restated Employment Agreement supersedes and replaces the CEO’s prior employment agreement, as amended and previously filed with the Securities and Exchange Commission (the “Prior Agreement”).

The Company entered into the Restated Employment Agreement primarily to make the form of the CEO’s employment agreement consistent with the employment agreements for the Company’s other executives, increase the CEO’s salary, adjust his benefits in connection with a Change in Control, eliminate additional income tax “gross-up” payments in connection with a Change in Control provided for in the Prior Agreement, and to meet current market practices. Capitalized terms used but not defined herein have the meanings ascribed to them in the Restated Employment Agreement.

Among other items, the material modifications to the terms of the Prior Agreement include the following:

The foregoing description of the Restated Employment Agreement does not purport to be complete and is qualified in its entirety by the Restated Employment Agreement, which is attached hereto as Exhibit 10.2 and incorporated herein by reference.

Item 9.01Financial Statements and Exhibits.

(d)Exhibits.

SIGNATURES

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