With just one week left in fiscal year 2025 (FY25), few expect Congress to pass the 12 appropriations bills necessary to fully fund the government in FY26. Although both the House and the Senate have advanced their own versions of some (but not all) of the bills, the two chambers have yet to start negotiations to resolve any differences between them, making it impossible that any bills will reach President Trump’s desk before September 30. Instead, Congress has shifted its focus to passing a continuing resolution (CR) to temporarily fund the government at FY25 levels. If Congress fails to pass a CR, the government will shut down on October 1.
Continuing Resolution
A CR is a temporary measure that funds the government at the previous fiscal year’s levels for a limited period, giving legislators more time to reconcile and pass the actual appropriations bills. If such a measure is not in place by the start of the new fiscal year, i.e., October 1, the government will shut down. The most recent shutdown occurred during the first Trump Administration, lasting a record 35 days between December 2018 and January 2019. CRs have been the norm for decades: Since 1977, at least one CR has been enacted in all but three fiscal years. Notably, Congress never actually passed its FY25 spending bills; instead, it passed a full-year CR, keeping funding at FY24 levels.
Last week, Representative Tom Cole (R-OK), Chair of the House Appropriations Committee (HAC), introduced H.R.5371-Continuing Appropriations and Extensions Act, 2026. This bill funds most programs at FY25 levels—with some exceptions—through November 21 or the enactment of the final FY26 appropriations bills. The House passed this bill on September 19 by a 217 to 212 margin: two Republicans voted against the bill, one Democrat voted for it, and three Representatives did not vote. The bill quickly moved over to the Senate that same afternoon but failed by a 44 to 48 margin, with two Republicans voting against it and another eight not voting at all. Senator Patty Murray (D-WA), Ranking Member of the Senate Appropriations Committee, offered an alternative bill—S.2882 – Continuing Appropriations and Extensions and Other Matters Act, 2026—to extend funding through October 31, but this failed to pass. Critically, a CR requires 60 votes to pass in the Senate (in order to end debate/a filibuster) and Murray’s bill received only 47 Yeas (all Democrats and Independents), which was not enough despite outnumbering the Nays.
Back in the House, Representative Rosa DeLauro (D-CT), Ranking Member of the HAC, introduced her own counterproposal, which would fund the government through October 31. However, Speaker Mike Johnson (R-LA) is unlikely to bring this proposal to the floor for a vote, as it repeals all the health-related cuts (including to Medicaid) from Trump’s One Big Beautiful Bill Act passed earlier this summer. Another sticking point for Democrats is the expiring Affordable Care Act tax credits—Democratic leadership has indicated they will only support a CR that extends these credits. Republicans, in contrast, want to pass a “clean” CR that makes few if any substantial changes to FY25 funding levels.
Both the House and Senate are eying a relatively short CR, lasting less than two months. In contrast, the Trump Administration has been pushing for a CR that expires on January 31, 2026, but lawmakers on both sides of the aisle have rejected this proposal
The State of Funding for Science Agencies
As of publication, both the House and Senate Appropriations Committees have passed their versions of the two bills most relevant to federal science agencies. The Commerce-Justice-Science (CJS) bills cover the National Science Foundation (NSF), while the Labor-Health and Human Services-Education (LHHS) bills cover the National Institutes of Health (NIH), the Advanced Research Projects Agency for Health (ARPA-H), and the Institute of Education Sciences (IES). Overall, the Senate recommended more money for each of the four agencies than the House did (see table below), with the biggest difference for NSF. Nevertheless, both chambers firmly rejected the steep cuts proposed by the Trump Administration earlier this year. It is unclear how long it will take the two chambers to resolve these differences. In the past, the final budgets usually end up somewhere between the House number and the Senate number.
| House | Senate | Difference | |
| NIH | 46,900 | 47,200 | 500 |
| ARPA-H | 945 | 1,500 | 555 |
| IES | 740 | 793 | 53 |
| NSF | 7,000 | 9,060 | 2,060 |
[FABBS Federal Science Funding Dashboard]
[For more information about these bills, see previous FABBS articles on the House and Senate CJS bills; House LHHS bill; and Senate LHHS bill.]
Moving Forward
Reporting out of Washington, DC suggests Congressional Republicans, Democrats, and the White House face an uphill battle in negotiating a CR. Complicating matters further, neither the House nor the Senate are in session this week, which have been designated District and State Work Periods. FABBS will continue to monitor the appropriations process and its impact on federal science agencies as well as work with coalitions to advocate for higher-level funding for these agencies (e.g., NIH community ask; NSF community ask; IES community ask).
