NBC- A federal judge in Boston on Wednesday ordered the Trump administration to unfreeze nearly $2.2 billion in federal grants to Harvard.

“All freezes and terminations of funding to Harvard made pursuant to the Freeze Orders and Termination Letters on or after April 14, 2025 are vacated and set aside,” U.S. District Judge Allison D. Burroughs said in the order.

The 84-page order conceded that Harvard has been “plagued by antisemitism” in recent years, and should “have done a better job of dealing with the issue,” but noted “there is, in reality, little connection between the research affected by the grant terminations and antisemitism.”

“In fact, 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, and did so in a way that runs afoul of the APA, the First Amendment and Title VI,” Burroughs wrote. Title VI prohibits discrimination based on race, color or national origin.

Harvard and the Department of Justice did not immediately respond to a request for comment.

The Trump administration said it’ll move to appeal the “egregious decision.”

The ruling comes after Harvard filed a lawsuit against the Trump administration after it announced in April it was freezing more than $2 billion in grants to the school because Harvard refused to comply with the administration’s demands that included auditing viewpoints of the student body.

On April 11, the Trump administration sent Harvard 10 demands that included restricting the acceptance of international students who are “hostile to the American values and institutions,” having a third part audit programs and departments “that most fuel antisemitic harassment or reflect ideological capture,” and shuttering all diversity, equity and inclusion programs and initiatives, including in hiring and admissions.

Burroughs said the Trump administration “failed to meet their burden” in showing it acted in a non-retaliatory way.

She cited that April letter in which the Trump administration conditioned funding on agreeing to those 10 terms, noting “only one of which related to antisemitism.” She said the other six terms were “related to ideological and pedagogical concerns, including who may lead and teach at Harvard, who may be admitted, and what may be taught.”

Burroughs said that while the defendants said the funding review was to combat antisemitism, the record found the Trump administration didn’t engage in any review of antisemitism on campus nor consider “if and how terminating certain grants would improve the situation for Jewish students at Harvard.”

Harvard ultimately received grant termination letters in early and mid-May from several federal agencies.

“None of the Termination Letters identified any specific instance of antisemitism on Harvard’s campus, specified how Harvard failed to respond to any such acts of antisemitism in a way that violated Title VI, or reflected any effort to follow the Title VI procedural requirements that govern the termination of federal funding,” Burroughs continued.

The judge also highlighted the impact the freeze and terminations have on grant recipients and research.

“Work has been ordered to stop on a vast number of research projects across fields that are critical both nationally and worldwide,” she wrote. “There is no obvious link between the affected projects and antisemitism.”

Burroughs vacated the grant freeze orders and termination letters as they relate to Harvard University, “as violative of the First Amendment.”

She also blocked the administration from issuing any other termination, fund freezes, stop work orders, or otherwise withholding payment on existing grants or other federal funding, or refusing to award future grants, contracts, or other federal funding to Harvard in retaliation for the exercise of its First Amendment rights, or on any purported grounds of discrimination without compliance with the terms of Title VI.

The White House appeared to defy the ruling, saying in a statement Wednesday: “Harvard does not have a constitutional right to taxpayer dollars and remains ineligible for grants in the future.”

“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,” White House spokesperson Liz Huston said.

The Department of Education rebuffed the ruling, calling it “unsurprising.”

“The same Obama-appointed judge that ruled in favor of Harvard’s illegal race-based admissions practices — which was ultimately overturned by the Supreme Court — just ruled against the Trump Administration’s efforts to hold Harvard accountable for rampant discrimination on campus,” said Madi Biedermann, deputy assistant secretary for communications at the department. “Cleaning up our nation’s universities will be a long road, but worth it.”

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