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): October 25, 2012

BioMarin Pharmaceutical Inc.

(Exact name of registrant as specified in its charter)

Registrant’s telephone number, including area code: (415) 506-6700

(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 2.02 Results of Operations and Financial Condition.

On October 25, 2012, BioMarin Pharmaceutical Inc. (the “Company”) announced financial results for the third quarter ended September 30, 2012. The Company’s press release issued on October 25, 2012, is attached hereto as Exhibit 99.1 and is incorporated by reference herein.

In its press release, the Company presented net loss for the three and nine months ended September 30, 2012 and September 30, 2011, and financial guidance for 2012, both as determined in accordance with U.S. Generally Accepted Accounting Principles (“GAAP”) and on a non-GAAP basis. In the press release, the non-GAAP financial measures presented are based on GAAP Earnings Before Interest, Taxes, Depreciation and Amortization (EBITDA), adjusted to exclude non-cash stock compensation expense, non-cash contingent consideration expense and certain nonrecurring material items (Non-GAAP Adjusted EBITDA). The reconciliation of the non-GAAP financial measures to the comparable GAAP financial measures are included in the press release attached hereto as Exhibit 99.1.

The Company believes this non-GAAP information is useful to investors taken in conjunction with the Company’s GAAP information because it provides additional information regarding the performance of the Company’s core ongoing business, Naglazyme, Kuvan, Aldurazyme and Firdapse and development of its pipeline. By providing information about both the overall GAAP financial performance and the non-GAAP measures that focus on continuing operations, the Company believes that the additional information enhances investors’ overall understanding of the Company’s business and prospects for the future. Further, the Company uses both GAAP and non-GAAP results and expectations internally for its operating, budgeting and financial planning purposes and uses the non-GAAP Adjusted EBITDA methodology in establishing corporate goals for internal compensation programs.

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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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