FDA Commissioner Resigns Just Before FDA's Budget Hearing

Why It Matters

The Senate Appropriations Subcommittee on Agriculture, Rural Development, Food and Drug Administration, and Related Agencies convenes tomorrow for an FDA budget hearing examining the agency's fiscal year 2027 funding request, a session that arrives at one of the most turbulent moments in the agency's recent history.

The session immediately follows the resignation of FDA Commissioner Marty Makary, who stepped down after privately stating his opposition to the FDA's approval of flavored vapes, according to the New York Times. The move came after weeks of pressure and rumors that President Trump was going to fire him, Politico reported.

The Trump administration is asking Congress to approve $7.2 billion for the FDA, a $215 million increase over the prior year, even as the agency is still rebuilding from workforce reductions driven by the Department of Government Efficiency. What senators decide to fund, and what they choose to scrutinize, will shape whether the agency responsible for drug approvals, food safety, and medical device oversight can restore the capacity it lost.

A Budget Built on Disruption

The FDA's fiscal year 2027 budget justification lands before the subcommittee against a backdrop of institutional strain. The agency entered the current fiscal year with over $6.9 billion in total budget authority ($3.4 billion in discretionary funding and $3.6 billion in user fees) after Congress rejected the deeper cuts the administration sought for fiscal year 2026.

The FY2027 request now proposes a modest increase, but also includes a structural change that is likely to draw questions: the reorganization of the National Center for Toxicological Research from FDA to CDC, a shift that alters how the agency conducts safety science.

The broader administration budget context adds pressure. The FY2027 proposal includes $73 billion in cuts to domestic agencies, encompassing health and environmental programs across the federal government. The FDA's proposed increase is an exception to that pattern, one that Congress will weigh against an agency still working through the consequences of the past year's staffing disruptions.

DOGE's Lasting Mark on the FDA

Six days before the agriculture appropriations hearing, STAT News published a detailed account of what the FDA lost in the year since DOGE's cuts, with six agency staffers describing work they never expected to leave. That reporting, combined with earlier accounts of the cuts' scope and execution, frames the stakes of the FDA budget justification hearing in concrete terms.

The scale of the reductions was significant. FedScoop reported that HHS moved to cut roughly 10,000 workers across the department, and that FDA technology officials who cooperated with DOGE's data requests were still subjected to staff reductions.

The FDA had approximately 18,000 employees before the cuts, according to reporting from BioPharma Dive, which quoted James Shehan, chair of the FDA Regulatory Practice at law firm Lowenstein Sandler, describing the cuts as "haphazard and sloppily implemented" and warning that "there's no indication that the cuts are done."

The fallout was immediate in some areas. Fortune reported that the FDA scrambled to rehire entire teams overseeing medical devices after DOGE eliminated them, with termination letters rescinded following pushback from the medical device industry, which pays the agency hundreds of millions in user fees annually.

Food Navigator USA reported in February 2026 that the cuts raised food safety risks, with affected employees including those who approve drug labels, post recall notices, and test food and drug samples, all functions within the subcommittee's direct oversight jurisdiction.

Who Has Been Lobbying

Industry groups and companies with direct stakes in the FDA's budget and operations have been active on Capitol Hill in the year leading up to the hearing.

The Medical Device Manufacturers Association spent $1.2 million across the past four quarters lobbying specifically on "MDUFA implementation; FDA staffing," and "appropriations and user fee funding for the Food and Drug Administration," a consistent focus that maps directly onto the questions this hearing will surface about whether the agency has adequate staff to administer the user fee programs that fund a significant portion of its operations.

The Alliance for a Stronger FDA spent $205,000 over the same period on FDA congressional budget and appropriations issues, with its most recent first quarter 2026 filing specifically referencing "Fiscal Year 2027 Food and Drug Administration Appropriations." The American Brain Coalition similarly shifted its most recent filing to FY2027 Agriculture, Rural Development, and FDA Appropriations.

The Personalized Medicine Coalition spent $170,000 lobbying on "FY2027 Food and Drug Administration Budget Priorities" for the agency's drug and device centers, while Pharmavite LLC spent $160,000 advocating for "adequate budget and staffing for FDA for dietary supplement oversight."

B. Braun Medical Inc. spent $354,000 across three quarters on "FDA issues, generic pharmaceutical and medical device issues, drug and device shortage issues," a portfolio that reflects the supply chain vulnerabilities that staffing disruptions can accelerate.

Altria Client Services spent $150,000 on FDA budget, appropriations, and authorization issues. Food companies, including Schwan's Co. and Johnsonville Sausage maintained consistent lobbying on FDA food activities and food safety throughout the year.

In total, organizations with direct interests in the FDA's budget and operations disclosed more than $4.2 million in lobbying expenditures on related issues over the past year.

The Subcommittee's Leadership

Sen. John Hoeven (R-N.D.) chairs the subcommittee, with Sen. Jeanne Shaheen (D-N.H.) serving as ranking member. The hearing is scheduled for Wednesday, May 13. No witness list has been released ahead of the session.

The questions senators ask (and the answers the administration provides) will signal how Congress intends to approach an agency that is simultaneously being asked to do more with a modestly larger budget while still accounting for what it lost.

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