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Reopening the FDA and USDA

After 43 days, the longest government shutdown in U.S. history is officially over. On November 12, 2025, the President signed H.R. 5371, the Continuing Appropriations, Agriculture, Legislative Branch, Military Construction and Veterans Affairs, and Extensions Act, 2026, reopening the federal government and restoring funding across agencies. (Business Insider)

The package combines full-year FY 2026 appropriations for Agriculture–FDA and related agencies with a continuing resolution (CR) through January 30, 2026 for the rest of the government. (Holland & Knight) It also fully funds SNAP and other nutrition programs for the fiscal year, reversing weeks of turmoil for food assistance.

This post closes out our shutdown series by focusing on two questions clients are asking today:

1. What exactly was the damage at FDA and USDA?
2. Now that the lights are back on, what operations resume—and how fast?

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1. The Damage: 43 Days of Lost Time

FDA: frozen fees, stalled reviews, silent inboxes

From October 1 through November 12, FDA operated under its contingency plan and the Anti-Deficiency Act. The agency repeatedly confirmed that during the lapse it could not accept new FY 2026 user-fee submissions—covering PDUFA, BsUFA, GDUFA, MDUFA, OMUFA, ADUFA/AGDUFA and many tobacco and device fees. (U.S. Food and Drug Administration)

Practically, that meant:

• No new fee-requiring submissions were accepted (NDAs/BLAs/ANDAs, many 510(k)s and De Novos, OMORs, etc.).
• Routine inspections, meetings, and non-urgent communications were deferred, with only limited “exempt/excepted” public-health activities and carryover-funded work continuing. (HHS)
• CTP and CVM relied on carryover and excepted staff but still saw slowed reviews, postponed meetings, and uncertainty around deadlines. (HHS)

Sponsors effectively lost six weeks of calendar time for fee-paying submissions at a critical planning point for FY 2026.

USDA: nutrition chaos and inspection strain

On the USDA side, the shutdown collided with SNAP in a way we have never seen:

• SNAP funding lapsed on November 1, triggering litigation and a patchwork of partial, delayed, or blocked benefits until Congress restored funding. (Politico)
• Court orders briefly forced full or partial payments, while the Supreme Court’s emergency stays added further uncertainty. (The Washington Post)
• Food banks and states absorbed the shock, with USDA issuing conflicting guidance as the shutdown dragged on. (Politico)

Beyond nutrition programs, FSIS, APHIS, and AMS struggled to maintain inspection, permitting, and grading operations under limited funding and staffing, prioritizing only the most critical activities.

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2. What Reopens Now at FDA

With H.R. 5371 signed, the legal condition that blocked new FY 2026 user-fee intake is now satisfied. FDA’s own lapse guidance said it “will not have legal authority to accept user fees… until an FY 2026 appropriation or Continuing Resolution for the FDA is enacted.” That contingency has now occurred. (U.S. Food and Drug Administration)

Expect the following effective immediately or very shortly:

User-fee submissions

• Electronic gateways will resume accepting fee-requiring submissions, including:
  • NDAs/BLAs (PDUFA, BsUFA)
  • ANDAs and related submissions (GDUFA)
  • Most 510(k)s, De Novos, PMAs, and supplements with MDUFA fees
  • Outsourcing facility submissions (OMUFA)
  • ADUFA/AGDUFA applications for animal drugs
  • Many CTP submissions that carry user-fee implications

Sponsors who saw transactions rejected or blocked for payment validation during the lapse should be prepared to re-submit immediately, with fees queued and reconciled.

Reviews, meetings, and guidance work

• Review teams ramp back to normal staffing, relying on user-fee carryover and restored appropriations.
• Type B/C/D meetings (drugs/biologics), Q-Subs/513(g)/Pre-Subs (devices), controlled correspondence (generics), and tobacco meetings should resume scheduling.
• Guidance, policy, and enforcement activities that were paused can re-start, but with a backlog of pending work.

CTP and CVM

• CTP resumes regular PMTA/SE review, enforcement prioritization, and litigation support—especially important given ongoing tobacco and ENDS cases.
• CVM returns to normal timelines on animal drug submissions and related compliance, after weeks of relying primarily on carryover resources.

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3. What Reopens Now at USDA

Because the bill includes a full-year Agriculture–FDA appropriations division, USDA’s key programs are not merely on a short CR—they are funded for the entire fiscal year. (Holland & Knight)

SNAP and nutrition programs

• SNAP, school meals, and other child nutrition programs are fully funded for FY 2026, ending the extraordinary episode of litigation-driven, partial benefits. (People.com)
• USDA and state agencies will move to restore standard issuance schedules, reconcile partial payments, and unwind emergency workarounds.

FSIS, APHIS, AMS

• FSIS can restore full inspection coverage and address inspection backlogs, including missed or delayed verification tasks.
• APHIS resumes normal permitting, import/export certifications, and disease-surveillance activities.
• AMS returns to routine grading and marketing services, resolving delays that hit perishable products hardest.

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4. Backlogs and Delays: How Long Until “Normal”?

Yes—the blog should absolutely address backlog and timing. It’s the question every sponsor is already asking.

Experience from prior shutdowns—and early commentary on this one—suggests that “business as usual” does not resume overnight. Agencies face a surge of accumulated work, stressed staff, and compressed statutory timelines. (White Collar Law Blog)

FDA backlog dynamics

You can reasonably expect:

• Intake surge in the first 2–3 weeks as sponsors rush to file queued submissions and fee payments.
• Triage toward public-health and statutory-clock work (e.g., products with pending PDUFA goal dates, safety-related supplements, critical shortage mitigation).
• Cascading shifts in goal dates and meeting slots, especially for submissions that would have started their clocks during the shutdown.

Realistically, sponsors should plan for:

• At least several weeks of intake and scheduling turbulence, even for well-prepared submissions; and
• Downstream ripple effects lasting months for non-critical programs (e.g., discretionary meetings, non-urgent postmarket supplements, certain tobacco and animal-drug activities).

USDA backlog dynamics

At USDA, priority will likely be:

1. Stabilizing SNAP and other nutrition benefits—getting money out the door and cleaning up the litigation-driven confusion. (Senate Committee on Appropriations)
2. Restoring full inspection and permitting capacity at FSIS and APHIS, focusing on export-dependent and high-risk operations.
3. Clearing permit and grading queues that accumulated during staffing restrictions.

Here again, stakeholders should assume weeks of operational catch-up even though legal authority and funding are restored today.

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5. Practical Next Steps for Industry

For clients and readers, here’s the short checklist:

1. Re-file blocked submissions immediately.
   • Confirm fees, payment routing, and submission packaging (e.g., eSTAR, eCopy) are current and ready.
2. Re-confirm meetings and inspections.
   • Reach out to your FDA or USDA contacts about rescheduling cancelled meetings, inspections, or audits, and ask how the center/district intends to handle missed commitments.
3. Adjust internal timelines.
   • Build in conservative margin for approvals, clearances, or permits that were directly or indirectly paused during the shutdown.
4. Capture shutdown impacts in your records.
   • For QMS and compliance documentation, contemporaneously note where regulatory delays were caused by the federal lapse in appropriations.
5. Watch the next deadline: January 30, 2026.
   • For non-Ag/FDA agencies covered only by the CR, another funding cliff looms. While FDA and USDA are better-insulated thanks to full-year Ag–FDA appropriations, cross-agency dependencies (e.g., CDC, EPA, CMS) still matter for many products. (Holland & Knight)

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Closing Thoughts

This shutdown did more than furlough workers—it erased 43 days of regulatory time for FDA-regulated products and threw USDA’s nutrition and inspection systems into disarray. (Business Insider)

With H.R. 5371, Congress has finally restored funding and given FDA and USDA authority to act again. But the consequences will echo well into 2026 in the form of delayed launches, extended development timelines, and stressed public-health infrastructure.

If you need help triaging your submissions, revising timelines, or planning a post-shutdown regulatory strategy with FDA, CTP, CVM, or USDA, this is the moment to reassess—and to rebuild.