Government Shutdown Effects on Public Health: Lessons from the 2025 and 2018-2019 Closures
November 17, 2025 | Catherine Jones
When the federal government shuts down, it exposes vulnerabilities in our public health ecosystem. It also brings to light the critical role state and territorial health departments play to protect the health of their jurisdictions. While the political dynamics behind each shutdown may vary, the consequences are unfailingly disruptive. Some federal agencies and programs continue under mandatory or advance appropriations, but the day-to-day machinery that keeps the federal public health system functioning — workforce, oversight, and technical assistance — is impacted. Federal employees from shuttered agencies are either furloughed or required to work without pay if their roles are deemed essential to public safety, as with certain functions of HHS and FDA, among others.
The effects of a shutdown can be temporary or long-lasting. In the past, Congress enacted guardrails to reduce the harm of future funding lapses, but the unpredictable nature of each shutdown ensures that disruption, loss, and hardship follow. A comparison of the 2025 and 2018-2019 shutdowns displays this impact — with the 2025 impasse becoming the longest shutdown in U.S. history, surpassing the 35-day record set during the December 2018 to January 2019 closure.
Key Differences Between the Shutdowns
The 2018-2019 shutdown, which was sparked over a funding fight for the U.S-Mexico border wall, spared HHS because the FY2019 Labor-HHS-Education Appropriations Act had already been enacted before the funding lapse. As a result, core public-health agencies — including CMS, CDC, HRSA, and SAMHSA — continued operating. However, the programs funded through the Agriculture-FDA appropriations bill (e.g., SNAP, WIC, and FDA) were impacted, but the disruptions were somewhat contained: FDA paused some food and drug inspections, while SNAP and WIC administrators worked to stretch timing buffers to sustain benefits.
The 2025 shutdown, by contrast, impacted HHS. Disputes over the Continuing Appropriations and Extensions Act, 2026, (H.R. 5371), also known as a continuing resolution (CR) — compounded by an acrimonious stalemate over extending the Affordable Care Act premium tax credits (analyses show premiums could more than double in 2026 without extensions) and reversing Medicaid cuts in the One Big Beautiful Bill — placed health care directly in the shutdown’s epicenter.
After 14 failed attempts to move the CR in the Senate, the measure was revised to extend federal funding through Jan. 30, 2026, and to reverse the Reductions in Force (RIFs) enacted during the lapse in appropriations. This CR was combined with three additional minibus appropriations packages, which included the Agriculture-FDA bill that funds SNAP and WIC through FY2026. On Nov. 10, the Senate narrowly mustered the 60 votes needed for passage, with eight Democratic senators joining in support. The bill then cleared the House on Nov. 12 with a 222-209 vote, and President Trump signed it the same day.
The result of the 43-day shutdown was a deeper and more systemic breakdown. Furloughs and RIFs swept across agencies. Staffing gaps impacted CDC, SAMHSA, and CMS operations, while lawsuits proliferated over withheld pay, suspended contracts, and SNAP payment distribution. As of now, ACA subsidies remain unresolved, and the full repercussions of the 2025 shutdown continue to emerge.
A Closer Look at the Shutdown Impacts
Furloughs
In 2025, the HHS contingency plan anticipated furloughing roughly 41% of its workforce, with CDC and NIH hit hardest — about 64% and 75% of staff, respectively. During the 2018-2019 shutdown, about 48% of HHS staff were furloughed, with CDC at 61% and NIH at 76%.
After the 2018-2019 shutdown, Congress enacted the Government Employee Fair Treatment Act of 2019, ensuring that all furloughed federal employees receive retroactive back pay once operations resume. The current CR provides a provision requiring the payment of federal employees who are furloughed or excepted during the lapse. Government contractors, unlike direct federal employees, are not guaranteed back pay after shutdowns.
RIFs
During the 2025 shutdown, CDC issued more than a thousand layoff notices, some later rescinded, while SAMHSA reported significant workforce losses. There were no RIFs during the 2018-2019 shutdown.
In AFGE v. Donald J. Trump, federal-worker unions challenged the administration’s issuance of mass layoff notices during the 2025 shutdown, arguing that RIFs during a funding lapse violate the Antideficiency Act and are “arbitrary and capricious.” A federal judge issued a preliminary injunction blocking further RIFs for hundreds of employees. This case is currently ongoing. To note, as part of the revised aforementioned CR, RIFs issued during this shutdown were reversed, returning to status quo workforce levels prior to the lapse of appropriations.
WIC
WIC entered October 2025 with funds from Section 32, providing $300 million as a bridge. Nationally, on average, WIC (a discretionary program) needs about $150 million per week to serve approximately 7 million women, infants, and children. To support access, several states tapped emergency funds and reallocated resources to food banks. In early November, the Trump Administration transferred $450 million from unused customs revenue to fund WIC. During the 2018-2019 shutdown, WIC continued to operate without gaps using prior-year funds.
SNAP
Roughly 42 million Americans currently rely on SNAP benefits. SNAP is considered mandatory spending, which allows payments to continue temporarily during a shutdown, but when a lapse exceeds 30 days, disruption risk escalates.
During the 2025 shutdown, EBT payment delays triggered widespread litigation. In Coalition of States v. U.S. Department of Agriculture, over 25 states sued USDA for suspending benefits despite available contingency funds, citing violations of the Food and Nutrition Act and the Administrative Procedure Act. Federal courts issued temporary restraining orders protecting millions of beneficiaries. The administration appealed to the Supreme Court to halt payments, and the Court granted the request.
During the 2018-2019 shutdown, SNAP participants received benefits in December 2018 and January 2019. February benefits were also distributed in late January to avoid disruptions; these were not additional benefits.
Tribal Health
In 2025, the Indian Health Service remained open due to FY2026 enacted advance appropriations. This funding was in part a reaction to the dire consequences of the 2018-2019 shutdown in which the Tribal and Urban health programs reported having to limit health care services and resources, due to Indian Health Service employees having to work without pay or being furloughed.
Unique Implications of the 2025 Shutdown
As previously noted, because Congress fully funded HHS in 2018-2019 there was minimal impact on public health programs. However, the length and scope of the 2025 shutdown did impact HHS directly. For example:
- Mental health: Mental and behavioral health access contracted sharply as SAMHSA’s state-support network lost nearly two-thirds of its staff, due to shutdown RIFs as well as earlier rounds of layoffs and retirements.
- At-home care and telehealth: During the 2025 government shutdown, hospitals nationwide faced delayed Medicare reimbursements and the temporary suspension of hospital-at-home programs, which had become vital for managing capacity during workforce shortages. Telehealth expansion and remote monitoring efforts were also paused, causing many patients to pay out of pocket.
- U.S. territories: The pause on SNAP and the Nutrition Assistance Program (NAP) funding in November had disproportionate impacts on the U.S. territories, as higher percentages of their populations depend on SNAP and NAP (20%-40%). In three territories, legislatures passed bills to fund partial or full SNAP and NAP benefits for November.
Implications for the Future of Public Health
The 2025 shutdown underscored that lapses in government funding disrupt the public health ecosystem. A fully functioning system relies on steady collaboration from federal, state, local, and tribal health departments.
The depth of the 2025 crisis has ignited bipartisan discussion about structural fixes to prevent governing by brinkmanship. Proposed congressional legislation includes bills to stabilize federal pay with automatic funding, contain congressional travel and adjournment until appropriations are complete, guarantee pay for federal workers and contractors, prevent disruption to SNAP and WIC programs, and ensure reimbursement to states.