What an FY 2026 federal government shutdown will mean for FDA

What will continue at FDA

In case of a shutdown, user fee funded FDA activities, including those related to the “regulation of human and animal drugs, biosimilar biological products, and medical devices” will continue for as long as FDA has carryover user fee funds available. According to FDA’s plan, these activities will include work that supports the review and marketing authorization of pending medical products, review of requests to conduct “important clinical research,” issuance of certain guidances and regulations, and other “necessary activities” that help patients access therapies, diagnostics, vaccines, generics, and biosimilars. Regulation of tobacco products—funded entirely by user fees—will also continue. User fee funded activities will only continue for as long as carryover funds for a given program are available, so in the event of a long shutdown we may see certain product areas curtail user fee funded activities before other product areas, depending on the “runway” of carryover fees in each program. FDA does not generally make the runway for each program public.

Certain health and safety operations will likewise proceed. FDA will keep operating where needed to address imminent threats: responding to public-health emergencies, managing recalls, mitigating drug shortages, monitoring adverse events, reviewing import entries to triage health risks, and conducting for cause and certain surveillance inspections and related regulatory testing, along with essential criminal and selected civil investigations.

While the White House Office of Management and Budget is reportedly directing federal agencies to prepare for RIFs in the event of a shutdown, FDA appears to be following a familiar path to prior government shutdowns. FDA anticipates retaining about 13,872 staff (86%) during a lapse, including roughly 10,740 “exempt” employees (66%) funded by sources like carryover user fees and 3,132 “excepted” (19%) performing life/property protection or necessarily implied functions. Other staff are expected to be furloughed.

What will slow down or stop at FDA

Many FDA activities will slow down or stop. FDA will not be able to accept new user fee funded submissions while appropriations are lapsed. These include new and abbreviated new drug applications, biologics license applications, 510(k)s/PMAs/De Novos, animal drug applications, and other submissions that require a user fee payment.

FDA will “immediately halt most unapproved prescription drugs activities” and will also limit many routine inspections. As noted, FDA can continue with for cause inspections and those that are needed to address imminent threats to the safety of human life, as well as those that can proceed with carryover user fee funding.

In general, FDA will pause some of its “regulatory science research,” potentially disrupting studies, as well as “longer-term policy development.” Investments in laboratory equipment and hiring will be delayed.

A familiar playbook

FDA’s approach to an FY 2026 shutdown mirrors prior years: continue tasks related to imminent threats to the safety of human life and user fee funded activities, while pausing discretionary or longer-horizon activities. HHS’s FY 2025 plan described the same core approach and specifically highlighted FDA’s continued emergency response, recall support, import screening, and other critical functions during a lapse.

However, in the wake of many FDA staff departures in recent months, one factor that may distinguish this potential funding gap from prior years is the agency’s reduced workforce. With a reduced capacity, and FDA resources being devoted to shutdown planning and to furloughs, it remains to be seen how the government may be able to cope with additional budgetary constraints this year.

Practical implications for industry

• For sponsors with active review files: If your application is already under review and supported by carryover user fees, expect continued FDA engagement, though responsiveness may vary as review teams manage staffing constraints and the administrative burdens. Build in buffer for routine interactions and non-critical information requests.
• For teams planning submissions: FDA says it will not accept user fee required submissions during the lapse, which will delay clock starts and downstream milestones (advisory meetings, launch planning, financing milestones).
• For manufacturers and importers: Maintain heightened quality and supply chain vigilance. While FDA will continue for cause and certain surveillance inspections and import screening, routine oversight will be thinner; a significant quality signal could draw rapid attention even amid the lapse. Ensure recall playbooks and shortage mitigation protocols are current.
• Button up FDA interactions: Respond promptly to outstanding FDA information requests or additional data holds so your file isn’t left in limbo if staff availability tightens. Resolve minor issues or clarifications—now, if possible—because non‑critical back‑and‑forth may slow during a lapse. Confirm meeting logistics or timelines for any scheduled meetings, so you know whether they’ll proceed or need rescheduling.

If appropriated funding lapses, FDA will keep critical health and safety functions running and continue user fee‑funded activities, but it will not accept new fee‑bearing submissions, and many routine activities will pause.

If you have questions about how to continue productive engagement with FDA during a shutdown, please contact the authors or your usual Hogan Lovells regulatory counsel.

Authored by Lynn Mehler, Randy Prebula, and Elizabeth Jungman