Federal Judge Rules Trump Administration Illegally Froze $2.2 Billion in Harvard Research Funding

People walk through Harvard Yard on the Harvard University campus in Cambridge, Massachussetts, April 15, 2025.

Joseph Prezioso/AFP via Getty Images

September 3, 2025 – Boston, MA – In a landmark decision, U.S. District Judge Allison D. Burroughs ruled on Wednesday that the Trump administration unlawfully froze $2.2 billion in federal research grants to Harvard University, marking a significant legal victory for the Ivy League institution. The ruling, delivered in Boston’s federal court, found that the administration’s actions violated Harvard’s First Amendment rights and federal law, accusing officials of using allegations of campus antisemitism as a pretext for a broader ideological assault on one of America’s premier universities.

The dispute began in April 2025, when the Trump administration, through its Joint Task Force to Combat Anti-Semitism, issued a letter to Harvard demanding sweeping changes to the university’s admissions, governance, hiring practices, and academic programs. These demands included auditing student and faculty viewpoints, restricting international student enrollment, and dismantling diversity, equity, and inclusion initiatives. When Harvard President Alan Garber rejected these conditions as an overreach of federal authority and a violation of the university’s autonomy, the administration swiftly froze $2.2 billion in multi-year grants and $60 million in contracts, impacting over 900 research projects.

In her 84-page opinion, Judge Burroughs, an Obama appointee, sharply criticized the administration’s rationale, stating, “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.” She noted that the frozen funds supported critical research in fields like medicine, science, and technology, including studies on Alzheimer’s, cancer, heart disease, and programs aiding veterans’ mental health. Burroughs emphasized that there was “little connection” between the funded projects and the administration’s stated concerns about antisemitism, adding that the freeze could harm the very communities it claimed to protect, including Jewish researchers and those studying diseases like Tay-Sachs.

The judge ruled that the administration’s actions violated Harvard’s First Amendment protections by retaliating against the university for refusing to comply with demands that infringed on its academic freedom. Additionally, she found the freeze to be “arbitrary and capricious” under the Administrative Procedure Act and non-compliant with Title VI of the Civil Rights Act, as the government failed to investigate specific instances of antisemitism tied to the affected research or consider Harvard’s existing efforts to address campus concerns. Burroughs vacated all freeze orders and termination letters issued since April 14, 2025, and barred the administration from imposing new funding restrictions in retaliation for Harvard’s exercise of its constitutional rights.

Harvard’s lawsuit, filed in April, argued that the funding cuts threatened vital research with far-reaching consequences for public health and national innovation. The university highlighted projects like tuberculosis research led by Professor Sarah Fortune and work on the Epstein-Barr virus’s link to multiple sclerosis, which received the Breakthrough Prize in Life Sciences. “This ruling affirms Harvard’s First Amendment and procedural rights and validates our arguments in defense of the university’s academic freedom, critical scientific research, and the core principles of American higher education,” President Garber said in a statement to the Harvard community.

While the decision is a major win for Harvard, the only university to sue over the administration’s funding freezes, the White House signaled its intent to appeal. Spokesperson Liz Huston called the ruling “egregious,” claiming, “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.” The Education Department echoed this sentiment, with spokesperson Madi Biedermann referencing Burroughs’ prior ruling in favor of Harvard’s race-based admissions, which was later overturned by the Supreme Court.

Burroughs acknowledged in her ruling that Harvard “has been plagued by antisemitism in recent years and could (and should) have done a better job of dealing with the issue.” However, she concluded that the administration’s demands, which included ideological screenings and governance overhauls, were “untethered from antisemitism” and aimed at controlling the university’s academic direction. The judge also rejected the administration’s argument that the case should be handled by a specialized contract court, asserting that it involved “bedrock constitutional principles” rather than mere contractual disputes.

The ruling could bolster Harvard’s position in ongoing settlement talks with the White House, though tensions remain high. President Trump has publicly demanded “nothing less than $500 million” from Harvard and threatened further actions, including revoking the university’s tax-exempt status and restricting international student enrollment. Other universities, like Columbia, have settled similar disputes, with Columbia agreeing to pay $221 million to restore funding. Harvard, however, has taken a defiant stance, framing the fight as a defense of academic freedom and institutional autonomy.

The decision has sparked widespread discussion on X, where users have debated the balance between combating campus antisemitism and preserving free speech. Some posts applaud Harvard’s resistance, with one user stating, “This is a win for academic freedom against government overreach.” Others criticized the university, arguing it has not done enough to address antisemitic incidents. The ruling also drew support from groups like the American Association of University Professors and the Foundation for Individual Rights and Expression, which hailed it as a victory for higher education and free thought.

As the Trump administration prepares to appeal, the case underscores a broader clash over the role of federal funding in shaping university policies. For now, Harvard’s research programs, which account for nearly half of its budget at schools like the T.H. Chan School of Public Health, are poised to resume with restored funding, though the long-term outcome remains uncertain.