What the First Circuit Is Really Deciding

• The First Circuit is weighing whether a federal judge had the power to restore billions in Harvard research funding after finding the government acted unlawfully.
• The Trump administration says the dispute belongs in the Court of Federal Claims because, at bottom, Harvard is seeking federal money.
• Harvard says the case is much bigger than a contract dispute—it claims the government used federal funding to retaliate against constitutionally protected resistance.

By Samuel López | USA Herald

BOSTON — The latest courtroom battle between President Donald Trump’s administration and Harvard University may look like a fight over billions of dollars in research grants.

Legally, something larger is happening.

The U.S. Court of Appeals for the First Circuit heard arguments Monday over whether a federal district judge could block the administration’s termination of Harvard research funding after finding the government retaliated against the university for refusing demands involving hiring, admissions, governance and academic viewpoints.

U.S. District Judge Allison Burroughs ruled on September 3, 2025, that the administration’s funding freeze violated Harvard’s First Amendment and statutory rights. Her 84-page ruling addressed nearly $2.2 billion in initially challenged grants, while later funding actions pushed the amount affected above $2.6 billion.

But the Justice Department has found a potentially powerful appellate argument; maybe Burroughs was the wrong judge in the wrong court to order the money restored.

Government attorney Michael Velchik told the three-judge panel that disputes seeking payment under federal grants belong in the U.S. Court of Federal Claims. In his words, the district court lacked jurisdiction to effectively require the government to keep paying Harvard.

That argument matters because the Supreme Court has recently signaled that ordinary federal district courts may lack authority to order payment on terminated federal grants when the dispute is essentially contractual. In separate 2025 cases involving Education Department and NIH grants, the Supreme Court treated the Court of Federal Claims as the likely forum for claims centered on the government’s obligation to pay grant money.

Harvard, however, is trying to draw a critical line.

Its attorney, former U.S. Solicitor General Paul Clement, argued that Harvard is not merely saying, “You breached our grants, give us the money.” Harvard says the government used funding as punishment after the university refused to accept federal demands.

“These are not claims that really depend on the contract,” Clement told the court. He argues that these are claims against retaliatory discrimination.

The government argues Harvard failed to adequately address antisemitism on campus and says taxpayers are not required to continue financing institutions that tolerate discrimination. Harvard does not deny serious antisemitism problems existed. The fight is over whether those concerns legally justified terminating unrelated scientific and medical research grants—and whether proper civil-rights procedures were followed first.

Judge Sandra Lynch appeared particularly skeptical of the government’s process, pointing out that there were no formal findings or completed investigation preceding the mass terminations.

Trump-appointed Judge Joshua Dunlap pressed Harvard from the other direction, questioning whether Burroughs’ ruling amounted to an order compelling the federal government to pay money—exactly the type of relief the administration says belongs elsewhere.

That is why this case reaches well beyond Cambridge.

If the government wins broadly, future administrations could have a stronger argument for moving federal-grant disputes out of ordinary district courts even where recipients allege unconstitutional retaliation.

If Harvard prevails, the ruling could confirm that the government cannot avoid First Amendment scrutiny simply by characterizing an alleged retaliatory funding cutoff as a contract dispute.

The First Circuit panel—Lynch, Gustavo Gelpi and Dunlap—did not rule from the bench. The case is President and Fellows of Harvard College v. U.S. Department of Health and Human Services, No. 25-2230.

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