How Harvard’s epic fight with Trump is costing the university

One of Harvard University’s biggest federal funding streams is down sharply, according to a New York Times analysis of government data.

The declines have persisted even after a federal judge forced the Trump administration to reverse drastic cuts to the university last year.

The funding, from the National Institutes of Health, currently lags about 18% behind the average pace of grants during the Biden administration, the analysis shows.

Last year, Harvard successfully sued the Trump administration, after the government announced it had frozen more than $2.2 billion in 2025, from multiple federal agencies.

But unlike then, when Trump officials made a public spectacle out of announcing the cuts, the NIH is mainly delaying, reducing, or rejecting grant requests, often leaving researchers and university leaders in the dark about what is happening.

The reduction appears to be the latest front in the Trump administration’s on-again, off-again war with Harvard and other elite universities. It is a new, more subtle tactic that is harder to fight in court, but that could be just as damaging if cuts and uncertainty build.

The Trump administration has targeted a number of the nation’s elite universities, accusing them of tolerating antisemitism and pursuing racial diversity in ways that flout the law, among other criticisms. Harvard — the country’s wealthiest university — has been one of the most frequent targets of federal officials.

As the Trump administration has pulled multiple levers to try to bring Harvard and other schools to heel, Harvard has often pushed back. It was the first institution to sue the Trump administration, has won in court on a number of occasions, and has not reached a settlement with the federal government, as other prominent schools have done.

Now, however, the university faces cuts that may be harder to counter. Last September, a judge ruled that the administration had improperly cut off funding to Harvard when it ended all of its grants in 2025, finding that the government had violated Harvard’s First Amendment rights.

But in the ruling, the judge suggested that there were lawful means the government could pursue if it wanted to restrict Harvard’s money, should it choose to.

That is what is happening.

Through June 30 of this fiscal year, which began Oct. 1, the NIH provided Harvard 309 awards worth a total of $200 million. The amount is down from an average of roughly 440 awards worth $246 million for the same nine-month period in 2021-2024, according to the latest data available.

Harvard is still one of the largest recipients of NIH funding, though it is far behind the top grantees such as Johns Hopkins, the University of Michigan, and Yale University. Other major research universities have also seen reductions in NIH funding.

Though NIH support has slowed compared with the Biden years, the 2026 awards are outpacing last year, when Harvard’s funding was frozen. By the same point in 2025, NIH funding to Harvard was stalled at 201 grants worth $94 million.

In recent months, Harvard’s individual schools have laid off staff. The leadership of the university’s largest division, the Faculty of Arts and Sciences, reported in an email to the division on Aug. 14 that 165 of its staff positions had been eliminated in a layoff and restructuring. The job cuts were aimed at reducing a major deficit.

Carrie Barbash, an organizer and former president of the Harvard Union of Clerical and Technical Workers, said the final number of layoffs may change as some staff members whose jobs were eliminated consider moving into some newly designed roles.

The current grant slowdown is not taking place evenly across Harvard. The university’s Chan School of Public Health is heavily dependent on NIH funds and has seen nearly 25% less in grant funding this year, compared with the average amount from 2021 to 2024.

The NIH has obligated $67 million across 63 awards to Chan through June of this fiscal year; the 2021-24 average for the same time period was $90 million across more than 100 awards.

Nancy Krieger, a professor of social epidemiology at the Chan School, said that fallout from the funding slowdown goes beyond individual projects that lost grants. More than a year of federal cuts — and legal fights over the reductions — have “shaken any sense of stability as to whether the federal government is a reliable funder,” she said.

The school is already cutting back, with layoffs and reductions in the number of slots for Ph.D. students. “It’s not just that you lost funding, it’s that you’re reducing the size of the cohort for the next generation of researchers that you’re training,” Krieger said. “What is the knowledge lost? And what are the myriad ripple effects for the economies of the cities and towns that depend on universities as major employers?”

Harvard has also won some rounds in its fight with the administration. Harvard’s court victories protected much of its grant money and its ability to host international students.

A federal judge on Aug. 13 dismissed a Trump administration lawsuit against Harvard that had accused the school of tolerating antisemitism and sought the ability to deny it grants.

Harvard’s endowment continues to ride the stock market to record highs, and the university’s steadfastness under pressure has inspired supporters and alumni who do not want it to yield to President Donald Trump.

While Yale is in talks to perhaps become the next elite school to settle with the administration, Harvard continues to hold out. Harvard is not believed to be engaged in any serious settlement talks at this time.

“Harvard is fighting for principles, both legal and constitutional, and doing so on behalf of the entire system of colleges and universities,” said Lee Bollinger, the former president of Columbia University. “We should all be grateful.”

Yet, as Bollinger noted, “any litigant will inevitably pay a high price.”

The administration has pushed the fight to Harvard on several fronts. The university is still engaged in other litigation and appeals with the Trump administration; a loss in any major case could be devastating.

The Trump administration continues to open fresh battles. The government is proposing new budget rules that would give the administration’s political appointees more power over grants.

White House spokesperson Liz Huston blamed the ongoing battles between the university and the administration on Harvard’s “stubborn commitment to unlawfully discriminating on the basis of race and failing to properly protect its students.”

“Unless Harvard comes to the table in good faith, the Trump administration will continue pursuing every available legal avenue to enforce federal civil rights laws,” she said.

Facing the uncertainty caused by lawsuits, grant slowdowns, and other pressures from the administration, Harvard and other schools are likely to continue to retrench, said Tom Gerety, a former president of Amherst College.

“The main thing you do in uncertainty is hunker down and say, ‘What cuts can we make right now?’” he said, noting that research universities are already trimming back on Ph.D. programs.

Tighter research budgets will mean scientists are more likely to seek jobs outside the United States, he said, while those still at American schools may be less likely to take the unconventional big swings in their research that can lead to scientific breakthroughs.

“This is going to hurt,” Gerety said, “and it’s going to hurt a lot more in 10 years than it does now.”

The government has pursued appeals of federal court rulings that went Harvard’s way last year.

The two sides, as well as a number of outside parties, filed briefs this summer over last fall’s decision in the funding case. The government is also appealing a June 2025 court decision blocking the administration’s effort to stop Harvard from hosting international students. Oral arguments in that case are scheduled for October.