FDA & USDA Reopening: What Likely Resumes on Day 0, Day 3, and Day 7 (Assuming CR Passage)

Assuming Congress passes and the President signs the pending continuing resolution

• FDA authority to accept user-fee submissions returns immediately upon enactment. During the lapse, FDA explicitly lacked legal authority to accept FY 2026 user-fee submissions; a CR/appropriation removes that barrier and normal intake can reopen. (U.S. Food and Drug Administration)
• FDA centers will pivot from contingency footing to normal operations, with triage toward public-health priorities and restoration of routine review, meetings, and compliance work as backlogs are sequenced. HHS/FDA contingency materials frame that pivot. (hhs.gov)
• USDA programs (FNS, FSIS, APHIS, AMS) should revert from partial/contingency guidance to standard operations as funding flows; states will receive FNS updates superseding November contingency memos. (USDA Food and Nutrition Service)

Backlog and Recovery Timeline: Even after funding is restored, both FDA and USDA face operational backlogs. Expect a staged recovery—FDA typically clears urgent submissions (recalls, safety-critical reviews) within the first week, while standard user-fee submissions and inspections may take two to four weeks to normalize. USDA field and inspection services often resume faster, but permit processing and state coordination (e.g., SNAP issuances) can lag several days. Sponsors should anticipate minor response delays through the end of the month.

Bottom line for sponsors and operators: prepare submissions now (cover sheets, fee payments, eCopy/eSTAR), line up meeting requests, and confirm inspection/permit schedules so you can move the moment the bill is signed.

Day-by-Day: What to Expect

Day 0 (Enactment → first 24 hours)

• FDA intake reopens for fee-requiring submissions across programs (PDUFA, BsUFA, GDUFA, MDUFA, OMUFA, ADUFA/AGDUFA). FDA’s FY 2026 lapse page is clear: no authority to accept FY 2026 fees during the lapse; enactment restores it. Expect gateways to re-enable payment/validation. (U.S. Food and Drug Administration)
• Centers shift off contingency plans. Mission-critical only → normalizing staffing, with internal directives prioritizing safety recalls, compliance deadlines, and statutory clocks. (hhs.gov)
• USDA signals reversion to standard operations. FNS should supersede its November SNAP contingency update; FSIS and APHIS communicate inspection coverage and permitting cadence. (USDA Food and Nutrition Service)

Days 1–3

• Submission acknowledgments & goal-date hygiene. FDA begins clearing queued payments/acknowledgments and clarifies treatment of any paused clocks. (Inference based on prior reopenings and current contingency posture.) (hhs.gov)
• CTP & CVM ramp. Tobacco PMTA/SE review correspondence resumes; CVM leans on carryover-funded continuity to accelerate back to pre-lapse cadence. (U.S. Food and Drug Administration)
• USDA field operations normalize. Expect FSIS to restore routine inspection coverage and APHIS to clear ePermits backlogs; FNS coordinates with states to resume standard SNAP issuance schedules. (Sequencing inferred; follow USDA/FNS bulletins to confirm timing). (USDA Food and Nutrition Service)

Days 4–7

• Meetings & interactions return to rhythm. Type B/C/D meetings (CDER/CBER), Q-Subs/513(g)/Pre-Subs (CDRH), controlled correspondence (OGD), and standard guidance/outreach cadence pick up.
• Public “operations resumed” notices. Expect short agency posts and center FAQs, including how to re-queue items that failed fee validation during the lapse. (Pattern inferred; monitor FDA/USDA homepages.)

Center-Specific Notes

• Human/biologics drugs (CDER/CBER): Expect rapid re-enablement of fee intake and acknowledgment steps. PDUFA plans underscore reliance on fee collections and the need to stabilize intake quickly. (U.S. Food and Drug Administration)
• Devices/Diagnostics (CDRH): eSTAR/RTA triage will matter—clean packaging moves first. Fee-dependent submissions (e.g., many 510(k)s, De Novos) should clear payment checks promptly after enactment. (U.S. Food and Drug Administration)
• Generics (OGD/GDUFA): Controlled correspondence and ANDA intake ramp as fee authority returns; GDUFA reserves help, but normal processing depends on restored appropriations. (U.S. Food and Drug Administration)
• Tobacco (CTP): PMTA/SE communications resume; watch for updated timelines where reviews were slowed by the lapse. (General contingency context). (hhs.gov)
• Veterinary (CVM/ADUFA/AGDUFA): Carryover cushions helped maintain some continuity; with funding restored, meeting queues and reviews should accelerate. (U.S. Food and Drug Administration)
• USDA:
  • FNS (SNAP): November memos on partial/contingency operations will need replacement; states should pivot back to standard issuance and admin processes once new guidance posts. (USDA Food and Nutrition Service)
  • FSIS/APHIS/AMS: Expect normal inspection, permitting, and grading services to resume with priority for perishable/export-linked work. (Confirm via agency bulletins.)

Indsutry Checklist (Do-Now so you can file on Day 0)

1. Fee-blocked submissions: Re-validate Form FDA 3397/cover sheets, payment routing, and submission packaging (eCopy/eSTAR). Have payment ready to post the hour enactment is signed. (U.S. Food and Drug Administration)
2. Meeting requests: Draft Type B/C/D, Q-Sub/513(g), and tobacco scientific advice requests now; have proposed agendas and questions polished for immediate submission.
3. Labeling & supplements: Queue clean updates you held during the lapse (annual reports, CBE-30, efficacy supplements, special 510(k)s) to enter the queue early.
4. Inspections & QA: Reconfirm audit windows, site readiness, and CAPA commitments; ask district/center contacts how they will handle slipped deadlines under the lapse. (hhs.gov)
5. USDA operations:
   • SNAP retailers/states: Monitor FNS for the superseding memo and align issuance calendars. (USDA Food and Nutrition Service)
   • Meat/poultry/egg processors: Touch base with FSIS on your inspection schedule; verify export library and PHIS notices once posted.
   • Importers/biologics/animal products: Check APHIS ePermits queues and VS import requirements as staff return.

What We’re Watching in the Final Text

• Effective date & duration. Funding duration determines how much “catch-up” is feasible before the next deadline. (We will update once the enrolled CR text is signed.)
• Program-specific anomalies. Any carve-outs affecting FDA/USDA operations, fee authority, or state program funding flows will drive sequencing.
• Staffing signals. HHS/FDA contingency ratios inform how quickly centers can unwind backlogs and resume guidance/communications. (hhs.gov)

Caveat (Until Signature)

This roadmap is contingent on enactment. As of this post, FDA still lacks authority to accept new FY 2026 user-fee submissions and USDA is operating under November contingency guidance in several areas. We’ll update the post header the moment the bill is signed and official “operations resumed” notices publish. (U.S. Food and Drug Administration)

Sources

• FDA: FY 2026 Lapse in Funding Information (authority to accept FY 2026 user-fee submissions upon enactment). (U.S. Food and Drug Administration)
• HHS: FDA Contingency Staffing Plan and HHS-wide Plan (who works during a lapse; ramp-back implications). (hhs.gov)
• USDA/FNS: SNAP Benefit & Admin Expense Update for November 2025 (will need superseding reopening memo post-CR). (USDA Food and Nutrition Service)
• FDA User-Fee Financial Plans (context on carryover and reserves for PDUFA/GDUFA/ADUFA). (U.S. Food and Drug Administration)