Boston Judge Rules in Favor of Harvard, Trump Administration Plans to Appeal

You win some and you lose some and this is definitely a loss, though perhaps a temporary one, for the Trump administration. A judge in Boston has ruled that the Trump administration must restore $2 billion in funding to Harvard.

A federal judge on Wednesday gave Harvard University a landmark victory in its fight against the Trump administration, siding with the Ivy League school in its effort to restore more than $2 billion in federal funding for research frozen by the White House.

The decision from US District Judge Allison Burroughs rejects the administration’s argument that it was targeting the university due to antisemitism on the school’s campus.

“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,” wrote Burroughs, an appointee of former President Barack Obama.

“Their actions have jeopardized decades of research and the welfare of all those who could stand to benefit from that research, as well as reflect a disregard for the rights protected by the Constitution and federal statutes,” Burroughs added…

“There is no obvious link between the affected projects and antisemitism,” the judge said.

So it’s a big win for now but this is definitely not the end of this particular battle or the administration’s larger war with universities. This decision will be appealed.

“To any fair-minded observer, it is clear that Harvard University failed to protect their students from harassment and allowed discrimination to plague their campus for years,” said Liz Huston, a White House spokeswoman. “Harvard does not have a constitutional right to taxpayer dollars and remains ineligible for grants in the future.”

She added that the government would “appeal this egregious decision, and we are confident we will ultimately prevail in our efforts to hold Harvard accountable.”…

The most obvious grounds for appeal is Judge Burroughs side-stepping of a recent Supreme Court decision.

More recently, [the Trump administraion] urged the judge to consider the implications of an August decision by the Supreme Court in a different case. In that case, which also concerned federal grants, the court ruled that challenges to individual terminations should be brought in the Court of Federal Claims. But it was a muddled ruling that left the door open for policy challenges in federal district courts.

Judge Burroughs acknowledged the Supreme Court’s decision on Wednesday and said she was “endeavoring” to follow it, but she largely asserted her own court’s jurisdiction.

So far, Harvard hasn’t commented. They may be looking to downplay this a little bit rather than do a victory lap, because they know an appeal of this is coming and also because there are still plenty of other ways the Trump administration can pressure Harvard even if the school eventually wins this battle.

The NY Times doesn’t say this but it seems likely that this one left-leaning judge in the Harvard’s hometown may be a bit of a homer. Even the timing of her decision seems to have been dictated by protecting Harvard from the Trump administration.

Judge Burroughs’s decision arrived at a moment of high tension for Harvard. Federal regulations had the university preparing to submit “closeout” paperwork for some terminated grants on Wednesday.

Without a ruling by Wednesday, the university had warned the judge, it feared that “the government will take the position that no restoration of funds is possible.”

And there’s reason beyond this one decision to think this judge’s judgment on Harvard is a bit one-sided.

I wonder if even the First Circuit will affirm this (admittedly thorough) ruling. While it is chock full of facts, the Supreme Court has clearly indicated that it is skeptical of district courts second-guessing Presidential grant cutting. We shall find out!

— Eric W. (@EWess92) September 3, 2025

A bit of a pattern is forming:

🚨 This is a clear-cut case of judge shopping. Obama-appointed Allison Burroughs has presided over five major cases involving Harvard—and sided with Harvard every single time.

– Blocked DHS from revoking Harvard’s Student and Exchange Visitor Program certification.

– Struck… pic.twitter.com/m9RZBSWOUZ

— Bad Hombre (@joma_gc) September 3, 2025

• Blocked DHS from revoking Harvard’s Student and Exchange Visitor Program certification.
• Struck down the 2020 ICE policy that would have deported international students taking only online classes.
• In April 2025, blocked the Department of Energy’s cap on indirect cost rates for Harvard grants.
• In 2019, upheld Harvard’s discriminatory affirmative action admissions policies—later overturned by SCOTUS.
• Just ruled to unfreeze $2.2 billion in federal grants for Harvard.

Last word to John Podhoretz:

I wish my dog were as loyal to me as Judge Allison Burroughs is to Harvard.

— John Podhoretz (@jpodhoretz) September 3, 2025

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