In a landmark decision that’s already sending ripples through the world of higher education, a federal judge has ruled that the Trump administration’s freeze of $2.2 billion in research funding for Harvard University was illegal, finding that the move violated constitutional protections and federal law. The ruling, handed down by U.S. District Judge Allison Burroughs on September 3, 2025, not only restores a vast sum of research dollars, but also reignites debate about free speech, academic independence, and the government’s role in policing campus culture.
The legal battle began in April 2025, when the Trump administration abruptly froze Harvard’s federal grants and $60 million in contracts. The administration justified the freeze by citing allegations, raised by its Joint Task Force to Combat Anti-Semitism, that Harvard had failed to adequately address antisemitism on campus. The move came just hours after Harvard rejected a set of government demands that included ending its diversity, equity, and inclusion programs and screening international students for ideological biases—including antisemitism. According to CBS News, the government’s letter listed ten conditions for continued funding, but only one directly addressed antisemitism; the majority focused on admissions, governance, and teaching policies.
Harvard swiftly challenged the funding freeze in court, arguing that it amounted to retaliation for the university’s refusal to comply with reforms that, in their view, violated First Amendment protections. In her sweeping 84-page order, Judge Burroughs sided with Harvard and employee groups, concluding that the administration “used antisemitism as a smokescreen” to unlawfully block billions in research funding. She wrote, “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.”
The judge’s criticism was not reserved for the government alone. She acknowledged that Harvard “has been plagued by antisemitism in recent years and could (and should) have done a better job of dealing with the issue.” Still, she found that the administration’s true motivation for the funding freeze was rooted in power and political views, not a genuine effort to combat antisemitism. “There is, in reality, little connection between the research affected by the grant terminations and antisemitism,” Burroughs noted in her decision, as reported by ABC News.
The ruling underscores the importance of safeguarding academic freedom and First Amendment rights, even in the face of intense government pressure. “Now it is the job of the courts to similarly step up, to act to safeguard academic freedom and freedom of speech as required by the Constitution, and to ensure that important research is not improperly subjected to arbitrary and procedurally infirm grant terminations, even if doing so risks the wrath of a government committed to its agenda no matter the cost,” Burroughs wrote. She further warned, “If speech can be curtailed in the name of the Jewish people today, then just as easily the speech of the Jews (and anyone else) can be curtailed when the political winds change direction.”
According to The Hill, the Trump administration’s legal team had argued that Burroughs, an Obama appointee, lacked the authority to hear the case, pointing to recent Supreme Court decisions that allowed the administration to terminate grants in other areas. Burroughs rejected this argument, critiquing the Supreme Court’s lack of clarity but affirming her commitment to uphold the law. She found that the administration’s actions “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.”
The impact of the funding freeze was far-reaching. As detailed in CNBC, Harvard was forced to halt work on a vast number of research projects, including studies on tuberculosis, NASA astronauts’ radiation exposure, Lou Gehrig’s disease, and predictive models to help Veterans Administration emergency room physicians assess suicidal veterans. “There is no link between the affected projects and antisemitism,” Burroughs observed, highlighting the arbitrary nature of the freeze.
While the decision marks a major victory for Harvard, Judge Burroughs’ ruling is not without caveats. She reiterated that “Harvard was wrong to tolerate hateful behavior for as long as it did,” but maintained that the administration’s focus was not genuinely on fighting antisemitism. “Even an indisputably worthy goal, however, does not allow Defendants to change course on decades of federal funding for critical research without providing a reasoned explanation as to how the agency determined that freezing funding would advance that goal, or, in other words, help combat antisemitism.”
The ruling also comes amid a broader pattern of conflict between the Trump administration and Harvard. In addition to the funding freeze, the administration attempted to prohibit Harvard from enrolling international students—a move also blocked by Judge Burroughs and now under appeal by the Justice Department. The administration has further threatened to revoke Harvard’s tax-exempt and accreditation status, and, as reported by CBS News, was in negotiations with Harvard leadership over a possible $500 million payment.
Reaction to the court’s decision has been sharply divided. The White House, through assistant press secretary Liz Huston, called Burroughs an “activist Obama-appointed judge” and vowed to appeal. “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. Harvard does not have a constitutional right to taxpayer dollars and remains ineligible for grants in the future,” Huston said, expressing confidence that the administration would ultimately prevail in holding Harvard accountable.
On the other side, Harvard’s President Alan Garber, speaking at the time of the freeze, asserted, “No government — regardless of which party is in power — should dictate what private universities can teach, whom they can admit and hire, and which areas of study and inquiry they can pursue.” Higher education leaders across the country have watched the case closely, viewing Harvard as a bellwether in the ongoing struggle between academic independence and governmental oversight.
Burroughs’ order vacates the freezing orders and bars the Trump administration from enforcing them, paving the way for the release of the $2.2 billion in research funding. Both Harvard and the Justice Department had requested a direct ruling without a trial, and Burroughs obliged, framing her decision as a necessary step to “act to safeguard academic freedom and freedom of speech as required by the Constitution.”
As the legal saga continues—now likely to move to appellate courts—the case stands as a stark reminder of the delicate balance between fighting hate and preserving fundamental freedoms. The judge’s words linger: “Combatting antisemitism is, without question, a laudable and important goal. But it cannot come at the expense of the First Amendment.”
The coming months will reveal whether the Trump administration’s appeal succeeds, but for now, Harvard’s research—and the principle of academic freedom—has won a significant reprieve.
