Congress has set the National Institutes of Health budget at $48.7 billion for fiscal year 2026, a $415 million increase over 2025, after rejecting President Donald Trump's request to slash the agency by more than 40%. Trump signed the appropriations package on Tuesday.

The bill includes modest increases for cancer ($128 million), Alzheimer's ($100 million) and ALS ($15 million) research. It also bars the administration from reimposing a 15% cap on indirect research costs — a policy that, had it stood, would have saved the government an estimated $4 billion annually. An appeals court affirmed a lower-court block on that cap last month.

"Congress has essentially rejected the president's very dramatic cuts," said Joanne Padrón Carney, chief government relations officer for the American Association for the Advancement of Science. "In past years, we might not consider flat funding to be a success, but considering how we're operating this past year, I think we're quite pleased."

How much damage did 2025 inflict before the reversal?

The funding picture obscures a turbulent year inside the federal research enterprise.

• More than 10,000 STEM-trained federal employees left government service.
• About half of NIH's 27 institute and center director positions remain unfilled.
• A JAMA Internal Medicine study found grant terminations affected clinical trials with 74,000 participants.
• NOAA and NASA together lost thousands of staff.
• The National Weather Service is not flying its full complement of weather balloons, raising questions about forecast accuracy.

NIH grant processing collapsed in early 2025. Thousands of awards were stalled, delayed or terminated. By late spring the agency had spent so little of its $36 billion extramural allocation that Jeremy Berg, a University of Pittsburgh computational and systems biology professor who tracks NIH outlays, said "NIH was getting way behind." Republican senators wrote to the Office of Management and Budget in July demanding the agency disburse the funds, warning the slowdown "risks undermining critical research."

NIH then shifted to awarding full four- or five-year grant commitments at once rather than annually. Berg called the maneuver "really mostly an accounting trick," and noted NIH funded roughly 5% to 10% fewer projects in 2025 than under normal patterns.

What role did the courts play?

A year ago, Georgetown University's Health Policy and the Law Initiative tracked zero federal science funding cases. By February 2026, that number stood at 39. "It exploded," said Katie Keith, the initiative's director.

Notable rulings:

• A judge ordered the unfreezing of $2.2 million in Harvard grants.
• A federal judge dismissed a faculty-union case seeking to restore about $400 million in Columbia University grants (now on appeal).
• The ACLU reached a partial settlement in December requiring NIH to resume review of paused grants, though litigation over cancelled DEI-related awards continues.

"The lawsuits have been a very important check," said Olga Akselrod, an ACLU attorney. "But I think that public health research remains at threat."

Columbia separately paid a $200 million settlement to restore federal funding after anti-discrimination allegations. Trump said Feb. 2 his administration will seek $1 billion from Harvard. Both matters remain in litigation.

What changed in lab workflow and personnel?

Even with the funding rebound, universities report lasting damage to research pipelines and faculty capacity.

At the University of Washington, a top-five NIH-funded public institution, the number of doctoral students entering the medical school fell by a third in fall 2025 as principal investigators questioned whether grant streams would continue. International doctoral applications dropped 5%. The university imposed a hiring freeze, travel restrictions and furloughs.

Shelly Sakiyama-Elbert, vice dean for research and graduate education at UW School of Medicine, described the year as "whiplash." She said the uncertainty "really distracts folks from doing their work, doing the science."

Will the FY26 money reach laboratories?

The legislation mandates monthly NIH reporting to Congress on grant awards, terminations and cancellations. Toby Smith, senior vice president at the Association of American Universities, said the provision reflects "strong bipartisan support for the federal government playing a critical role in supporting research."

Smith, however, flagged execution risk. "Yes, we've got the money now from Congress. Will they move it out the door? Will they have the staff to do that effectively?" About 13 NIH institute and center director posts remain unfilled, and an August 2025 executive order still requires senior political appointee approval for many grants.

The administration's FY26 request had proposed cutting NSF by 57% and NASA by 24%. Final appropriations trim NSF by 3.4% and NASA by 1.6%, according to AAAS.

Whether the legislative firewall holds against further indirect-cost challenges, grant pauses and personnel erosion will shape whether FY26 delivers the stability R&D managers spent 2025 hoping to see.