Trump administration appeals ruling restoring $2.7B in federal funding to Harvard

Why Harvard may have an 'uphill battle' in Trump admin funding fight

Fox News correspondent Molly Line and former deputy assistant attorney general John Yoo discuss President Donald Trump cutting funding to Harvard in his latest effort to crack down on antisemitism across college campuses on 'America Reports.'

Lawyers for the Trump administration said Friday they are appealing a judge’s order to restore $2.7 billion in frozen federal research funding to Harvard University, the latest twist in a months-long, high-profile court fight that has pitted the administration against the nation’s oldest and wealthiest university.

At issue is a ruling issued in September by U.S. District Judge Allison D. Burroughs, which blocked the Trump administration's attempt to terminate the more than $2 billion in federal funding for Harvard, which she said violated its First Amendment and due process protections.

"A review of the administrative record makes it difficult to conclude anything other than that defendants used antisemitism as a smokescreen for a targeted, ideologically-motivated assault on this country’s premier universities," Burroughs said in a blistering, 84-page order. She described the actions as tantamount to "an ideologically-motivated assault."

"We must fight against antisemitism, but we equally need to protect our rights, including our right to free speech, and neither goal should nor needs to be sacrificed on the altar of the other," she added. 

News of the appeal revives a high-stakes court fight that has shaken, if not displaced, Harvard’s status at the uppermost echelons of higher education in the U.S. It comes as other private and public universities have also come under scrutiny by the administration, prompting fresh criticism that the administration is seeking to exercise undue influence over curriculum and leadership at major institutions.

CONTINUED COURT FIGHTS COULD PUT HARVARD IN UNWINNABLE POSITION VS TRUMP

Banners on the Harry Elkins Widener Memorial Library at the Harvard University campus in Cambridge, Massachusetts, on May 27, 2025. (Sophie Park/Bloomberg) (Sophie Park/Bloomberg)

Harvard sued the Trump administration in April over its attempt to freeze the federal funding, and argued in court that the actions amounted to an unconstitutional "pressure campaign" to influence and exert control over elite academic institutions.

"Ultimately, this is about Trump trying to impose his view of the world on everybody else," Harvard Law professor Noah Feldman said in a radio interview discussing the Trump administration's actions. 

The Trump administration, for its part, accused Harvard of "fostering violence, antisemitism, and coordinating with the Chinese Communist Party on its campus." 

Lawyers for the Justice Department argued it had "every right" to cancel the funding for Harvard after it failed to comply with its demands.

Trump officials had immediately vowed to appeal the lower court's ruling in September, but declined to provide a time frame as to when it would do so. The administration and university officials have also reportedly been engaged in negotiations, though the status of those efforts remains unclear. 

A spokesperson for Harvard told Fox News Digital that the court's September order reinstated "critical research funding that advances science and life-saving medical breakthroughs, strengthens national security, and enhances our nation’s competitiveness and economic priorities."

"We remain confident in our legal position," this person added.

The White House did not immediately respond to a request for comment on the appeal. 

 HARVARD, TRUMP BATTLE FOR BILLIONS IN FEDERAL FUNDS AS JUDGE WEIGHS NEXT STEPS

President Donald Trump is seen on Air Force One. (AP NEWSROOM)

The move follows a January blitz by the Trump administration of civil rights investigations into dozens of prominent universities. Harvard, for its part, was the first school to sue the Trump administration over its efforts — and the school argues it has been hit by punitive efforts and investigations the months since, which it argues is an act of retaliation. 

At least six federal agencies have launched investigations into Harvard this year, university officials said. The administration also previously sought to ban Harvard's ability to host international students by attempting to revoke its certification status under the Student and Exchange Visitor Program (SEVP) – a program led by the Department of Homeland Security that allows universities to sponsor international students for U.S. visas. (That action was temporarily blocked by a lower court.)

JUDGES V TRUMP: HERE ARE THE KEY COURT BATTLES HALTING THE WHITE HOUSE AGENDA

Harvard University President Alan Garber addresses the crowd during the 373rd Commencement at Harvard University.   ((Photo by Craig F. Walker/The Boston Globe via Getty Images))

Still, experts said the actions have not been without consequence for the university. Regardless of the court’s outcome, the efforts – including attempts to revoke the school’s SEVP certification – have created "a chilling effect" for international students at Harvard, Aram Gavoor, an associate dean at George Washington University Law School and former Justice Department attorney, told Fox News Digital earlier this year.

Even if the Trump administration loses on the merits of the case, Gavoor said, "there's a point to be argued that it may have won as a function of policy."

Meanwhile, any long-term financial fallout the university might suffer as a result remains to be seen. 

Harvard, in October, reported a budget deficit of $113 million for the fiscal year — its first deficit since the COVID-19 pandemic – and which the school's president attributed to the tumult and uncertainty created as a result of the protracted court fight.

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"Even by the standards of our centuries-long history, fiscal year 2025 was extraordinarily challenging, with political and economic disruption affecting many sectors, including higher education," Harvard President Alan Garber said in a statement. 

Breanne Deppisch is a national politics reporter for Fox News Digital covering the Trump administration, with a focus on the Justice Department, FBI and other national news. She previously covered national politics at the Washington Examiner and The Washington Post, with additional bylines in Politico Magazine, the Colorado Gazette and others. You can send tips to Breanne at [email protected], or follow her on X at @breanne_dep.