NEW YORK, United States (AFP) — A United States (US) judge ordered Wednesday that deep funding cuts by the Trump administration to Harvard University be overturned, after they were imposed over claims of anti-Semitism and bias at the Ivy League institution.

Harvard sued in April to restore more than $2 billion in frozen funds. The administration insisted its move was legally justified over Harvard’s alleged failure to protect Jewish and Israeli students, particularly amid campus protests against Israel’s war in Gaza.

The cuts to Harvard’s funding stream forced it to implement a hiring freeze while pausing ambitious research programs, particularly in the public health and medical spheres — pauses experts warned risked American lives.

“The Court vacates and sets aside the Freeze Orders and Termination Letters as violative of the First Amendment,” Boston federal judge Allison Burroughs said in her order.

“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.”

Burroughs pointed to Harvard’s own admissions in legal filings that there had been an issue of anti-Semitism on campus — but said that the administration’s funding cuts would have no bearing on the situation.

“It is clear, even based solely on Harvard’s own admissions, that Harvard has been plagued by anti-Semitism in recent years and could (and should) have done a better job of dealing with the issue,” she wrote.

“That said, there is, in reality, little connection between the research affected by the grant terminations and anti-Semitism.”

The judge, appointed by Democratic former president Barack Obama, said the evidence she had seen suggested Trump “used anti-Semitism as a smokescreen for a targeted, ideologically-motivated assault on this country’s premier universities.”

Both Harvard and the American Association of University Professors brought cases against the Trump administration’s measures, which were combined.

Trump has sought to have the case heard in the Court of Federal Claims instead of in the federal court in Boston, just miles away from the heart of the university’s Cambridge campus.

The Ivy League institution has been at the forefront of Trump’s campaign against top universities after it defied his calls to submit to oversight of its curriculum, staffing, student recruitment and “viewpoint diversity.”

Trump and his allies claim that Harvard and other prestigious universities are unaccountable bastions of liberal, anti-conservative bias and anti-Semitism, particularly surrounding protests against Israel’s war in Gaza.

The government has also targeted Harvard’s ability to host international students, an important source of income who accounted for 27 per cent of total enrollment in the 2024-2025 academic year.