Congress Blocks Trump's Massive NIH Funding Cut Proposal

Why It Matters

A new Congressional Research Service (CRS) report on National Institutes of Health (NIH) funding details in stark terms how divided the Trump administration and Congress were on the future of the nation's premier biomedical research agency — and how decisively lawmakers rejected the White House's vision, at least for now.

NIH funds more than 300,000 researchers at over 2,500 universities, hospitals, and research institutions. Nearly 82 percent of its budget flows outward as grants and contracts. When the administration proposed cutting that budget by more than 40 percent and eliminating entire research institutes, it wasn't just a budget fight — it was a direct challenge to the infrastructure underpinning American biomedical science.

Congress said no. But the administration's proposals haven't gone away, and the legal and policy battles over how NIH operates are ongoing.

The Big Picture

NIH Funding Trends Heading Into the Showdown

NIH appropriations have followed a long arc of growth and stagnation. Congress and the White House doubled the NIH budget between 1998 and 2003, pushing it from $13.7 billion to $27.2 billion. After that, funding growth slowed considerably, and in several years — including 2006, 2011, and 2013 — the agency's budget actually shrank in nominal terms.

From 2016 through 2023, NIH received annual increases, with the largest single-year jump coming between 2017 and 2018, when the program level rose by $3 billion, or 8.8 percent. But even with those increases, NIH's inflation-adjusted purchasing power never recovered to its 2003 peak. The CRS report notes that the 2026 enacted funding level is estimated to be 10.3 percent below that peak in constant dollars, using the Biomedical Research and Development Price Index.

In 2025, NIH was funded primarily through a full-year continuing resolution that largely held spending flat at 2024 levels, with one notable exception: a $280 million reduction to the NIH Innovation Account, which supports the Precision Medicine Initiative and the Brain Research Through Advancing Innovative Neurotechnologies Initiative. Total NIH program funding in 2025 came to $47.035 billion, a decrease of $276 million, or 0.6 percent, from the prior year. Including the Advanced Research Projects Agency for Health, the combined total was $48.535 billion.

The Administration's Proposal

Against that backdrop, the Trump administration's 2026 budget request landed as a jolt. The White House proposed a total NIH program level of $27.915 billion — a reduction of $19.1 billion, or 40.6 percent, from the 2025 level.

The proposal wasn't just a funding cut — it was a structural overhaul. The administration proposed eliminating four institutes outright: the National Institute of Nursing Research, the National Center for Complementary and Integrative Health, the Fogarty International Center, and the National Institute on Minority Health and Health Disparities. Nineteen remaining institutes and centers would have been consolidated into eight restructured entities. Two components — the National Institute of Environmental Health Sciences and the Advanced Research Projects Agency for Health (ARPA-H) — would have been moved out of NIH entirely.

Under the proposed structure, every one of the eight new institutes would have seen funding cuts ranging from 21 percent to 44 percent compared to prior-year levels. The Office of the Director faced the steepest proposed cut, at 44 percent.

NIH itself estimated that under the proposed funding level, the agency would have supported 4,312 new competing research grants, a 29.3 percent decrease from the 6,095 grants supported at the 2025 funding level, and far below the 10,086 competing grants funded in 2024. The administration argued in its budget documents that the restructuring would "create efficiencies within NIH that will allow the agency to focus on true science, and coordinate research to make the best use of federal funds."

Congress Pushes Back

Congress responded by doing almost the opposite of what the administration requested. The Consolidated Appropriations Act, 2026, signed into law on February 3, 2026, provided NIH with a total program funding level of $47.493 billion — an increase of $458 million, or 1.0 percent, from 2025, and $19.578 billion more than the administration had requested.

The enacted legislation maintained NIH's existing 24-institute structure without modification. It did not incorporate any of the proposed restructuring. ARPA-H received the same $1.5 billion appropriation as in 2025, bringing the combined NIH and ARPA-H total to $48.933 billion.

On the policy side, Congress also rejected two of the administration's signature operational proposals. The administration had sought to cap indirect cost reimbursements — the funds that cover facilities and administrative expenses for grant recipients — at 15 percent of direct costs. Congress not only declined to adopt that cap but went further, maintaining a longstanding provision that explicitly prohibits the Department of Health and Human Services from developing or implementing a modified approach to indirect cost rates.

That provision matters because the administration had already tried to implement the cap unilaterally. NIH announced the indirect cost policy in February 2025, but a Massachusetts federal court permanently enjoined it in April 2025. The First Circuit Court of Appeals upheld that injunction on January 5, 2026. The enacted appropriations language reinforced the court's ruling through statute.

Congress also constrained the administration's multiyear grants policy. The White House had proposed reserving half of NIH's budget for grants that fully fund multi-year projects upfront, rather than obligating funds incrementally each year. The enacted law capped multiyear grant obligations at the same level as 2025.

Political Stakes

For the administration, the 2026 appropriations outcome is a significant setback. The proposed restructuring and deep cuts were rejected by a Republican-controlled Congress, suggesting that even within the GOP, there is limited appetite for the scale of NIH reform the White House sought. The administration's indirect cost policy was blocked by both the courts and the legislature.

For Congress, the episode highlights the ongoing tension between executive branch efforts to reshape federal agencies through budget proposals and the appropriations process as a check on that authority. Lawmakers used the 2026 spending bill not just to fund NIH at near-prior-year levels, but also to affirmatively prohibit specific administrative actions.

For the research community, the 2026 enacted numbers provide near-term stability. But the underlying dynamic is unresolved. The administration's proposals remain a marker of its policy direction, and future budget cycles could revisit the same cuts and restructuring. Meanwhile, even with the 2026 increase, NIH's inflation-adjusted funding continues to lag behind its 2003 peak by more than 10 percent.

A separate subplot in the CRS report adds another dimension. The Government Accountability Office (GAO) found in August 2025 that NIH had obligated $8 billion less between February and June 2025 than it had in the same period in 2024, raising questions about whether funds were being withheld in potential violation of the Impoundment Control Act. CRS's own subsequent analysis found that NIH ultimately obligated close to 100 percent of its 2025 discretionary budget authority by the end of the fiscal year — but the episode underscored the degree to which the administration's approach to NIH spending had drawn legal scrutiny.

The Bottom Line

NIH Funding Survived 2026 — The Larger Battle Continues

Congress preserved NIH's structure and its funding level for 2026, rejecting the administration's proposed cuts and reorganization in nearly every respect. The enacted total of $47.493 billion is $19.6 billion more than the White House requested.

But the administration's budget proposals, the blocked indirect cost policy, and the mid-year spending slowdown that drew GAO scrutiny all point to a sustained effort to reshape how NIH operates and how much it spends. The 2026 appropriations cycle was a decisive round for Congress, but not a final one. The next budget cycle will test whether that outcome holds.

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