#1Second Quarter 2023 Earnings July 31, 2023 BIOMARIN Transforming Lives Through Genetic Discovery#22 Table of Contents Business Overview & Highlights 6 Q2 '23 Key Financial Metrics 7 2023 Outlook 9 Non-GAAP Reconciliations 10 BIOMARIN#3Forward-Looking Statements. 3 This non-confidential presentation contains forward-looking statements about the business prospects of BioMarin Pharmaceutical Inc. (Bio Marin), including, without limitation, statements regarding expectations of growth and profitability, expectations for results of operations and financial guidance for the full-year 2023 and BioMarin's clinical development and commercial prospects, including, without limitation, (i) the risk of competition and long-lived revenue streams for BioMarin's enzyme-based therapy products, (ii) the markets for ROCTAVIAN and VOXZOGO, the potential to leverage VOXZO GO in conditions beyond achondroplasia, such as hypochondroplasia. These forward-looking statements are predictions and involve risks and uncertainties such that actual results may differ materially from these statements. These risks and uncertainties include, among others, those factors detailed in BioMarin's press release issued July 31, 2023 and Bio Marin's filings with the Securities and Exchange Commission, including, without limitation, the factors contained under the caption "Risk Factors" in BioMarin's Annual Report on Form 10-K for the year ended December 31, 2022 as such factors may be updated by any subsequent reports including BioMarin's Quarterly Report on Form 10-Q for the quarter ended March 31, 2023. You are urged not to place undue reliance on forward-looking statements, which speak only as of the date hereof. Bio Marin is under no obligation, and expressly disclaims any obligation to update or alter any forward- looking statement, whether as a result of new information, future events or otherwise. BIOMARIN#4Non-GAAP Financial Measures This presentation includes both GAAP information and Non-GAAP information. Non-GAAP Income is defined by the Company as GAAP Net Income excluding amortization expense, stock-based compensation expense, contingent consideration expense, and, in certain periods, certain. other specified items, as detailed below when applicable. The Company also includes a Non-GAAP adjustment for the estimated tax impact of the reconciling items. For BioMarin's 2023 financial guidance, Non-GAAP Income is defined as GAAP Net Income excluding amortization of intangible assets, stock-based compensation expense, and certain other specified items that are typically highly variable, difficult to predict, and/or of a size that could have a substantial impact on the Company's reported operations for a period, and Non-GAAP Diluted EPS is defined by the Company as Non-GAAP Income divided by Non-GAAP diluted shares outstanding. Non-GAAP Income and its components are not meant to be considered in isolation or as a substitute for, or superiorto, comparable GAAP measures and should be read in conjunction with the consolidated financial information prepared in accordance with GAAP. Investors should note that the Non-GAAP information is not prepared under any comprehensive set of accounting rules or principles and does not reflect all of the amounts associated with the Company's results of operations as determined in accordance with GAAP. Investors should also note that these Non-GAAP financial measures have no standardized meaning prescribed by GAAP and, therefore, have limits in their usefulness to investors. In addition, from time to time in the future there may be other items that the Company may exclude for purposes of its Non-GAAP financial measures; likewise, the Company may in the future cease to exclude items that it has historically excluded for purposes of its Non-GAAP financial measures. Because of the non-standardized definitions, the Non-GAAP financial measure as used by Bio Marin in this presentation may be calculated differently from, and therefore may not be directly comparable to, similarly titled measures used by other companies. BIOMARIN#5BioMarin is a Best-In-Class Genetic Disease Company at an Inflection Point of Transformative Growth Solid, Profitable, "IRA-proof" & Growing Base Business Anchored by durable enzyme-based therapies producing nearly $2B of revenue and positive operating cash flows. Steady revenue growth across the portfolio High barriers to entry results in lower risk of competition and long-lived revenue streams New Large-market Launches Are Significant Near-Term Growth Drivers ■ VOXZOGO® is the first and only approved treatment for Achondroplasia - tracking to blockbuster status ROCTAVIAN™, approved in the U.S. and Europe, is a safe and efficacious one-time treatment alternative to chronic therapy for eligible adults with severe hemophilia A Profit margin expansion expected as new product revenue growth leverages world class infrastructure Best-In-Class Innovation Capabilities. ◉ ◉ ◉ ◉ Industry-leading R&D teams produced suite of eight internally-developed genetic-based commercial therapies. Fully-integrated and scaled biopharma capabilities: Discovery, Clinical, Regulatory and world-class Manufacturing Leveraging decades of genetic expertise in current age of rapid genetic disease discovery Exceptional development success rate applied to deep early-stage pipeline with most assets in Company history#6Second Quarter 2023 Key Business Highlights 6 Increasing Q2 Profitability and Gross Margin Improvement Driven by Robust VOXZOGO® Demand ☑$113 million in VOXZOGO revenues drove total BioMarin GAAP net income of $56 million and gross margin of 78.5% > Kil in the second quarter Record-breaking Revenues for the First Half of 2023, with 13% Year-Over-Year Growth Tracking to double-digit revenue growth and significant operating leverage, driving more than 30% growth in expected bottom-line profitability in full-year 2023 ROCTAVIAN ™ Approved in the U.S., the First and Only Gene Therapy for Adults with Severe Hemophilia A U.S. approval unlocks an additional 2,500 potential patients New Phase 3 Study with VOXZOGO in Second Indication (Hypochondroplasia) Announced Enrollment in the baseline, run-in arm of the study expected to begin in the fourth quarter of 2023 Uptake of VOXZOGO® Continued to Accelerate in Q2 Resulting in Increased FY23 Guidance Increased full-year 2023 guidance to between $400 million and $440 million from previous guidance of between $380 and $430 million BIOMARIN#7Second Quarter 2023 Key Financial Metrics (In millions, except percentage data) Reported Revenue Growth Revenue Growth1 GAAP Net Income Non-GAAP Net Income2 Excluding KUVANⓇ $595 $545 $56 $105 $534 $476 +12% +14% $28 +102% $77 +37% Q2 2022 Q2 2023 Q2 2022 1 Includes total revenues excluding revenues from KUVAN. 2 7 Q2 2023 Q2 2022 Q2 2023 Q2 2022 Q2 2023 Non-GAAP Income is defined by the Company as reported GAAP Net Income, excluding amortization expense, stock-based compensation expense, contingent consideration, and, in certain periods, certain other specified items. The Company also includes a Non-GAAP adjustment for the estimated income tax impact of reconciling items. Refer to Non-GAAP Information on slide 10 of this presentation for reconciliations to the comparable information reported under U.S. GAAP. BIOMARIN#8Second Quarter Year-to-Date 2023 Key Financial Metrics (In millions, except percentage data) Reported Revenue Growth Revenue Growth1 GAAP Net Income² Non-GAAP Net Income ³ Excluding KUVANⓇ $1,192 $149 $1,091 $1,053 $936 +13% +16% (-28%) $221 $176 $107 +26% YTD 2023 YTD 2022 Includes total revenues excluding revenues from KUVAN. YTD 2022 1 2 3 8 YTD 2023 YTD 2022 YTD 2023 YTD 2022 YTD 2023 GAAP Net income in the first half of 2022 included a $89.0 million net gain, net of taxes, related to the sale of the Rare Pediatric Disease Priority Review Voucher (PRV) the Company received from the U.S. Food and Drug Administration (FDA) in connection with U.S. approval of VOXZOGO. Non-GAAP Income is defined by the Company as reported GAAP Net Income, excluding amortization expense, stock-based compensation expense, contingent consideration, and, in certain periods, certain other specified items. The Company also includes a Non-GAAP adjustment for the estimated income taxim pact of reconciling items. Refer to Non-GAAP Information on slide 11 of this presentation for reconciliations to the comparable information reported under U.S. GAAP. BIOMARIN#9Full Year 2023 Guidance 9 (In millions, except per share and percentage data) Enzyme Products Revenue¹ ROCTAVIAN Revenue VOXZOGO Revenue Total Revenues Gross Margin % GAAP Diluted EPS Prior Guidance As of April 26, 2023 $1,700 $1,850 $50 - $150 $380 - $430 $2,375 - $2,500 77.5% -79% Current Guidance As of July 31, 2023 Unchanged Unchanged $400 - $440 Unchanged Unchanged Unchanged 35.5% -37.5% $165 - $215 $0.83 - $1.08 R&D % of Revenue 30% -32% SG&A % of Revenue 36% -38% GAAP Net Income $155 - $205 $0.78 - $1.03 Non-GAAP Net Income $360 - $410 Non-GAAP Diluted EPS2 $1.80 - $2.05 $1.85 - $2.10 1 Enzyme Products include ALDURAZYME®, VIMIZIMⓇ, NAGLAZYME®, BRINEURAⓇ, and PALYNZIQⓇ. 2 2023 GAAP and Non-GAAP Diluted EPS guidance assumes ~200 million shares. BIOMARIN $370 - $420#10Reconciliation of GAAP Reported to Selected Non-GAAP Adjusted Information (In millions) 1 10 Q2 2023 Q2 2022 GAAP Reported Net Income Adjustments $56.0 $27.7 Stock-based compensation expense - COS 4.7 4.8 Stock-based compensation expense - R&D 15.1 13.6 Stock-based compensation expense - SG&A 30.4 28.7 Amortization of intangible assets 15.6 15.6 Contingent consideration 0.9 Severance and employee termination benefits 1 (2.2) Income tax effect of adjustments (14.4) (14.5) Non-GAAP Net Income $105.2 $76.8 Represents change in estimates to severance and employee termination benefit charges in SG&A related to the Company's organizational redesign announced in October 2022. The Company recognized $23.0 million of expense related to severance and employee termination benefits in the second half of 2022. BIOMARIN#11Reconciliation of GAAP Reported to Selected Non-GAAP Adjusted Information (In millions) 1 2 YTD 2023 YTD 2022 GAAP Reported Net Income Adjustments $106.9 $148.5 Stock-based compensation expense - COS 9.1 9.1 Stock-based compensation expense - R&D 34.9 30.8 Stock-based compensation expense - SG&A 59.9 55.0 Amortization of intangible assets 31.3 31.2 Contingent consideration Gain on sale of non-financial assets 1 2.9 (108.0) Severance and employee termination benefits 2 (0.1) Loss on investment in equity securities: 12.6 Income tax effect of adjustments Non-GAAP Net Income (33.6) $221.0 6.2 $175.7 Represents the net gain in the first quarter of 2022 on the sale to a third party of the PRV the Company received from the FDA in connection with the U.S. approval of VOXZOGO. Represents change in estimates to severance and employee termination benefit charges in SG&A related to the Company's organizational redesign announced in October 2022. The Company recognized $23.0 million of expense related to severance and employee termination benefits in the second half of 2022. 3 Represents the impairment loss on investment in non-marketable equity securities recorded in Other income (expense), net in the first quarter of 2023. 11 BIOMARIN#12Reconciliation of GAAP Net Income to Non-GAAP Income and Dilutive EPS Guidance (In millions, except per share data) Net Income 2023 Guidance 1,2 Diluted Shares Diluted EPS GAAP Net Income and Diluted EPS $165 to $215 200 $0.83 to $1.08 Amortization of intangible assets 60 0.30 Stock-based compensation expense Severance and employee termination benefits Loss on investment in equity securities 200 1.00 (0.1) 0.00 12.6 0.06 Income tax effect of adjustments 3 (68) (0.34) Non-GAAP Income and Diluted EPS $370 to $420 200 $1.85 to $2.10 1 23 The adjustments/reconciling items included in this table are presented to facilitate the reconciliation of Non-GAAP Income and Non-GAAP Diluted EPS to their closest GAAP financial metrics, GAAP Net Income and GAAP Diluted EPS. The specific amounts included in each reconciling line item above represent approximations of the underlying adjustments from GAAP Net Income to Non-GAAP Income and from GAAP Diluted EPS to Non-GAAP Diluted EPS. Actual 2023 results for each reconciling line item may be different, in some cases materially, than the amounts listed above as a result of uncertainty regarding, and the potential variability of, those items. Certain amounts may not sum or recalculate due to rounding. Income tax adjustments represent the estimated income tax impact of each pre-tax non-GAAP adjustment based on the applicable statutory income tax rate. 12 BIOMARIN#13Second Quarter 2023 Earnings July 31, 2023 BIOMARIN Transforming Lives Through Genetic Discovery