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

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

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

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.

"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. 

Rep. Ilhan Omar, D-Minn., said she has no regrets about supporting the MEALS Act during the COVID-19 pandemic, despite the program becoming linked to Minnesota’s alleged $250 million "Feeding Our Future" fraud scheme.

"Do you regret pushing for that bill, the MEALS Act? Do you think it led to the fraud?" Nicholas Ballasy for Fox News Digital asked Omar on Capitol Hill.

"Absolutely not, it did help feed kids," Omar said.

Omar introduced the MEALS Act on March 11, 2020, to modify the Department of Agriculture's food and nutrition programs to allow certain waivers on requirements for school meal programs, including those that raised federal costs during school closures related to the pandemic.

WALZ URGES NOEM TO 'REASSESS' IMMIGRATION ENFORCEMENT STRATEGY IN MINNESOTA AFTER ALLEGED CITIZEN ARRESTS

Minnesota has faced scrutiny for alleged mismanagement of federal funds accessed through these waivers, including in distributing money for the "Feeding Our Future" program, which authorities believe to be the largest fraud scheme in the history of the pandemic. 

INSIDE MINNESOTA’S $1B FRAUD: FAKE OFFICES, PHONY FIRMS AND A SCANDAL HIDING IN PLAIN SIGHT 

The scheme exploited the U.S. Department of Agriculture’s decision to waive many of its standard requirements for the Federal Child Nutrition Program during the pandemic, including relaxing its requirement for non-school-based distributors to participate in the program.

Fox News Digital first reported on the status of the fraud in July. FBI Director Kash Patel described it at the time as "one of the worst" in Minnesota history — and as of November 2025, more than 75 individuals have been charged in connection with the scheme, according to federal prosecutors.

President Donald Trump has recently announced a flurry of new actions to crack down and investigate fraud schemes in Minnesota, which he has assailed as a "hub of money laundering activity," and cited as the basis of his decision to terminate deportation protections for hundreds of Somali migrants.

Senior Trump administration officials announced fresh investigations this month, including a new Treasury Department probe into how taxpayer dollars were allegedly diverted to the terrorist organization al-Shabaab, according to Secretary Scott Bessent. 

Trump and other officials have zeroed in on these alleged fraud schemes, arguing that the criminal activity is a result of mismanagement and "incompetence" from Minnesota Gov. Tim Walz, a Democrat and former vice presidential candidate.

'INCOMPETENCE OR DERELICTION': MINNESOTA LAWMAKER RIPS TIM WALZ AS STATE FRAUD LOSSES MOUNT 

"It’s not surprising that the president has chosen to broadly target an entire community," Walz said of Trump's efforts, adding, "This is what he does to change the subject." 

Conspirators falsely claimed to have served millions of meals during the pandemic, but instead used the money for personal gain. They also are accused of fabricating invoices, submitting fake attendance records and falsely distributing thousands of meals from hundreds of so-called food distribution "sites" across the state.

Some of the individuals are part of Minnesota's Somali diaspora, which is the largest in the U.S., though the ringleader of the scheme is not.

"Stealing from the federal government equates to stealing from the American people — there is no simpler truth," FBI's special agent in charge, Alvin Winston, told Fox News Digital in a statement. 

Charging documents show that roughly 300 "food sites" in the state served little or no food, with the so-called "food vendors" and organizations fabricated to launder money intended to reimburse the cost of feeding children.

FBI officials told Fox News that the investigation and resulting trials and indictments continue to impact the state, and have already touched off legislative reform in Minnesota.

They added that the investigation into the fraud remains ongoing, and that additional charges are expected, though they did not immediately share more details.

"The egregious fraud unveiled in the Feeding our Future case epitomizes a profound betrayal of public trust," Patel told Fox News Digital earlier this year. 

"These individuals misappropriated hundreds of millions in federal funds intended to nourish vulnerable children during a time of crisis, redirecting those resources into luxury homes, high-end vehicles and extravagant lifestyles while families faced hardship," he added.

Trump suggested earlier this month that Omar, who fled Somalia as a child, "shouldn't be allowed to be a congresswoman," prompting fierce backlash from some Democrats and from Minnesota's congressional delegation. 

Omar, for her part, said Trump's remarks were "vile." 

"His obsession with me is creepy," she said on social media. "I hope he gets the help he desperately needs."

ICE REJECTS OMAR CLAIM SON WAS PULLED OVER BY FEDS, PRESSED FOR CITIZENSHIP PROOF: ‘ABSOLUTELY ZERO RECORD’

Ballasy later pressed Omar about another incident dominating headlines.

"Congresswoman, the ICE director is saying now that your son was not pulled over by ICE. He's saying there's no evidence," Ballasy said to Omar on Capitol Hill.

The head of Immigration and Customs Enforcement (ICE) rejected a viral claim from Omar that her son was pressed for proof of U.S. citizenship by agency personnel after stopping at a Minnesota Target over the weekend.

Omar had told CBS’ Twin Cities affiliate that her son was subjected to a traffic stop-type encounter by ICE agents but was ultimately let go without further issue after he was able to produce a U.S. passport or passport card.

Acting ICE Director Todd Lyons pushed back on the assertion on Tuesday, telling Fox News Digital the incident never happened.

"How do they know that?" Omar countered. "How do they know that? Is he saying he has documentations of all the people they pulled over? Because we've been asking for that information. We haven't gotten it from them, so if ICE confirming now that they collect data and refusing to provide it to members of Congress, then that's an interesting admission."

"ICE has absolutely zero record of its officers or agents pulling over Congresswoman Omar’s son," Lyons said.

"It speaks volumes that Congresswoman Omar is leveling this accusation with absolutely zero proof."

Lyons called Omar’s comments to the local outlet a "ridiculous effort" to demonize federal law enforcement. He also said her rhetoric contributes to a spike in threats against ICE personnel, citing a 1,150% increase in assaults and an 8,000% increase in death threats.

When asked to respond to Lyons' comment, Omar told Ballasy, "Well, their crackdown has terrorized my community, so they need to stop."