To spend its budget, the N.I.H. made an unusual number of large lump-sum payments for many years of research, instead of its usual policy of paying for research one year at a time.

As a result of this quiet policy shift, the average payment for competitive grants swelled from $472,000 in the first half of the fiscal year to over $830,000 in the last two months.

While this might sound like a boon for researchers, it’s actually a fundamental shift in how grants are funded — one that means more competition for funding, and less money and less time to do the research.

And because these fully funded grants commit all of their money up front, it means the agency’s annual budget is divided into fewer projects, instead of being spread among a larger number of scientific bets.

The new policy directive came from the White House’s Office of Management and Budget, which in the summer instructed the N.I.H. to spend half of its remaining funds to fully fund research grants. In the past, the agency would do so only in special circumstances.

The White House has said this would “increase N.I.H. budget flexibility” by not encumbering its annual budget with payments to previously approved projects. It has said it plans to continue this policy in 2026, while proposing to shrink the agency’s budget by $18 billion, or nearly 40 percent. (The Senate and House rejected the White House’s proposed budget cuts, but have not yet agreed on the agency’s budget.)

“My sense of it was that the administration wanted to clear the decks,” said Sarah Kobrin, a branch chief at the N.I.H.’s National Cancer Institute, who said she was sharing her views, not those of the institute.

The new policy is being carried out as the Trump administration has tightened its hold over federal science funding. Earlier this year, it delayed reviewing grants in order to vet research by political appointees, culled projects that mentioned D.E.I. and fired thousands of employees or pressured them to retire early. (The N.I.H. lost nearly 3,000 employees this year, or about 14 percent of its work force, based on a New York Times review of the agency’s shutdown contingency plans.)

“They brought everything to a stop,” Dr. Kobrin said.

Nonetheless, the N.I.H. managed to spend most of its budget by the end of the fiscal year. “My colleagues did an outstanding job to work their butts off to approve things,” said Theresa Kim, a program officer at N.I.H.’s National Institute on Aging.

Something similar happened at the National Science Foundation, which is the second-largest federal funder of research at U.S. universities, after the N.I.H.

The N.S.F. started the year with funding delays caused by the Trump administration, and it lost about a third of its employees in layoffs or forced retirements. The agency ended the year awarding 25 percent fewer new grants.

Facing a proposed $5 billion cut to its $9 billion budget, the N.S.F. fully paid off many of the grants that were on its books, a strategy that employees called “paying down the mortgage.” It also paid for nearly all new awards upfront (though, unlike at the N.I.H., not necessarily for less time and money).

To draw these conclusions, The Times used public data to analyze nearly every competitive grant — over 300,000 in all — that the N.I.H. and the N.S.F. awarded since 2015, and interviewed many employees at these agencies.

Here’s what we found:

1. Fewer grants in every area of science and medicine

Together, the N.I.H. and the N.S.F. had a nearly $60 billion annual budget for funding future breakthroughs in science and medicine, about a quarter of which is typically spent on new grants or competitive renewals.

This year, both agencies made far fewer competitive awards:

The White House has said it is streamlining scientific funding by eliminating wasteful spending and cutting “woke programs” that “poison the minds of Americans.”

But the more than 3,500 fewer competitive grants from the N.I.H. this year touched every area of biology and medicine:

In practice, this means thousands of very competitive projects in areas like cancer, diabetes, aging, neurological disorders and public health improvements probably went unfunded in 2025.

Similarly, at the National Science Foundation, the roughly 3,000 fewer new grants encompassed reductions to every area of science (and the social sciences):

There were fewer new grants awarded in biology, geosciences, STEM education, computer science and engineering, math, physics, technology and innovation.

Only the office of the director awarded more new grants this year; it funds projects that don’t neatly fall into other categories. That growth was fueled by a previously established N.S.F. goal to expand fellowships at universities in regions that have historically received less federal funding.

The Trump administration has also taken the unusual step of canceling thousands of active health and science grants, citing a lack of overlap with its priorities.

The website Grant Witness has estimated that the administration canceled or froze 5,415 N.I.H. grants this year, of which roughly half have been reinstated through court cases or negotiations where universities have agreed to some of the administration’s demands. And it canceled or froze 1,996 N.S.F. grants, of which nearly a third have been reinstated, according to Grant Witness estimates.

2. More competition

It’s simple math: Fewer grants implies more competition for federal funding.

Take the category of research grants known as R01, the oldest and most prestigious grant that the N.I.H. awards. An acceptance or rejection can make or break a scientist’s career.

These grants fund topics such as studying the impact of e-cigarettes on brain health, modeling the movements of mice, or devising new methods to kill mosquitoes.

Last year, only one in six were funded. But this year, the agency awarded 24 percent fewer R01 grants.

This means fewer scientists had their research funded. Last year, the N.I.H.’s National Cancer Institute funded R01 applications from new investigators that fell in the top 10 percent based on scoring by the agency. But by the end of fiscal year 2025, it funded only the top 4 percent.

“Nobody believes that a fourth-percentile and a fifth-percentile grant are clearly of different quality,” Dr. Kobrin said. “It’s just not that precise a measurement.”

3. A drop in grants mentioning diversity

The Trump administration has prioritized eliminating research that involves diversity, equity and inclusion, and has eliminated hundreds of keywords related to diversity on federal websites.

A Times analysis found a steep reduction in the share of competitive N.I.H. grants whose titles or abstracts included flagged D.E.I.-related keywords (such as “equity,” “racial minority” or “underserved patient”) on a list shared by N.I.H. employees.

The data shows a big surge in these keywords after 2020, during the Biden administration.

While some of the decline in 2025 could be attributed to a change in the language that researchers use to describe their work, it also probably reflects a drop in research related to minority health. For example, the National Institute on Minority Health and Health Disparities awarded 61 percent fewer competitive grants this year, the steepest decline at any arm of the N.I.H.

N.I.H. employees said they did not receive clear guidance on how to determine if a project was D.E.I.-related. Instead, they were sent spreadsheets of grants that had been flagged for not complying with the Trump administration’s priorities.

“We’re constantly hearing that things have been flagged,” Dr. Kobrin said.

“Nobody wants to acknowledge what they were flagged for.”

4. Fewer fellowships for future scientists

The government provides critical funds for training new scientists through graduate student, postdoctoral and early-career fellowships and grants.

The N.S.F. has run a prestigious graduate research fellowship program since 1952. It funds three years of research for around 2,000 of the country’s top science graduate students.

This year, it awarded 536 fewer such fellowships. The government originally planned to eliminate 1,000 fellowships, but later added about 500 more after facing protests from scientists and academics.

The cut affected most fields, with fellowships in four areas — life sciences, psychology, STEM education and social sciences — being cut by more than half. Fellowships in computer science, an administration priority, grew by almost 50 percent.

There were also months of delays in publishing the fellowship application for next year, and new eligibility restrictions that exclude second-year Ph.D. students from applying, which may lower the numbers of fellowships in future years.

“This is an incredibly shortsighted and regressive change,” said Kevin Johnson, a former program director at N.S.F.’s geosciences directorate, because second-year graduate students are usually better prepared to conduct research.

“It sends a signal to future potential applicants that science is not supported and is not valued,” he said.

Early-career scientists are usually more reliant on federal funding because they have few alternatives to fund their research and training. Many go on to work in industry afterward, further fueling the economy.

In a 1945 report that led to the creation of the N.S.F., Vannevar Bush, who directed military research and development during World War II, argued that the government should invest in training the next generation of scientists to ensure American scientific progress.

But many experts worry that the recent funding cuts and budget reductions may threaten America’s role as a global scientific leader.

“I personally know many scientists in my field leaving the United States altogether,” Mr. Johnson said.