Special Edition: Breaking Down the District Court Ruling in Harvard v. HHS

1636 Forum’s Key Takeaways

What has happened in Harvard v. HHS to date?

What did Judge Burroughs actually rule for Harvard in her opinion?

How does SCOTUS’s NIH v. APHA ruling fit into all of this?

Why is AAUP part of Harvard’s ruling?

What is next?

While Judge Burroughs technically granted in part the government’s motion on a narrow procedural issue, holding that her court “lacks jurisdiction to review under 5 U.S.C. § 706(2)(A),” she still vacated both the Freeze Orders and the Termination Letters on other grounds. 

Specifically, she found the government’s actions violated the First Amendment (§ 706(2)(B)) and the statutory and procedural requirements of Title VI (§ 706(2)(C), (D)), so the Freeze Orders and Terminations Letters were voided nonetheless. 

This jurisdictional wrinkle ties back to the Supreme Court’s recent ruling in NIH v. American Public Health Association (APHA), where Justice Barrett’s controlling opinion held that challenges seeking to restore terminated grant money generally fall under the CFC, not Article III courts (i.e., district or circuit courts) like Burroughs’. 

Burroughs acknowledged that limit here, but distinguished Harvard’s case as fundamentally about unlawful directives and constitutional violations — not just repayment. She determined that distinction allowed her to still strike down the Freeze Orders and Termination Letters on other grounds.

Under federal civil procedure (Fed. R. Civ. P. 62 and Federal R. App. P. 8), a losing party can ask the trial judge (here, Judge Burroughs) to stay (pause) enforcement of her judgment while an appeal is pending. 

If Burroughs denies that request, the government can then ask the First Circuit for an emergency stay. Without a stay in place, the agencies would be expected to restore Harvard’s research funding even while the appeal is ongoing.

One issue lurking in the background is repayment. Courts sometimes consider whether plaintiffs (in this case, Harvard) could realistically pay back the government if it ultimately lost on appeal. As the Supreme Court noted in NIH v. APHA, repayment can be “irreparably” difficult once funds have already been spent by researchers and students. 

The government may raise the same concern here, arguing that the risk of Harvard being unable to repay later justifies a stay until the appeals process has run its course. 

Within hours of the ruling, the White House vowed to appeal. A White House spokeswoman said the government would “appeal this egregious decision, and we are confident we will ultimately prevail in our efforts to hold Harvard accountable.”

If the government appeals as it has indicated it will, the case will move to the First Circuit. If Harvard wins there too, the government could next take the fight to the Supreme Court. 

Given SCOTUS’s recent NIH v. APHA decision steering other federal funding disputes to the Court of Federal Claims (CFC), Harvard may struggle to find a sympathetic audience. Months from now (if not years), Harvard could find itself right back where it started — forced to reargue in the CFC that it was entitled to its research grants in the first place, procedurally just as Justice Barrett suggested in NIH v. APHA.

Beyond the appeals process, the administration could also work to block Harvard from receiving future federal funding. As White House spokeswoman Liz Huston said after the ruling: “Harvard does not have a constitutional right to taxpayer dollars and remains ineligible for grants in the future.”

Judge Burroughs devoted significant space to explaining why Harvard’s claims differ from those in NIH v. APHA in her view. Whereas APHA involved only “arbitrary and capricious” challenges, Harvard also raised First Amendment and Title VI claims. She emphasized that First Amendment claims are not money-mandating (and thus fall outside the scope of the CFC) and that Title VI expressly authorizes judicial review in Article III courts.

She also noted that dividing the case across different courts, as the Supreme Court did in APHA, would not work here. Harvard’s constitutional and statutory claims are intertwined, so they must be resolved together in her opinion. As she put it, “the logical and legal considerations underlying the APHA decision … do not graft cleanly onto Plaintiffs’ First Amendment and Title VI claims.”

University of Baltimore Law School Professor (and author of the textbook on 21st Century Government Contract Law) Charles Tiefer (JD ‘77) told 1636 Forum, “It is impressive that the judge found a way to thread the needle through the Supreme Court decision that went four justices one way, four justices the other way, and a straddle by Justice Barrett. While the administration defended on technical jurisdictional grounds, the judge showed that once she got beyond those, the administration pitch to take over the academic business was hollow.”

Judge Burroughs did not shy away from signaling her frustration with the Supreme Court’s recent emergency rulings. 

In one footnote explaining that she is “endeavoring to follow the Supreme Court’s reasoning in APHA,” before going on to distinguish her case, Burroughs notes that lower courts must follow Supreme Court precedent “no matter how misguided [they] may think [them] to be,” while adding that the grant-termination rulings “have not been models of clarity.” 

In the same footnote, Burroughs nodded to Justice Gorsuch’s admonition in his NIH v. APHA opinion that “Lower court judges may sometimes disagree with this Court’s decisions, but they are never free to defy them.” She stressed that she was not defying the Court but “endeavoring” to follow its reasoning while distinguishing Harvard’s case. The aside carries extra resonance in Massachusetts, since her colleague Judge William Young was the lower court judge accused of “defying” precedent in NIH v. APHA, an accusation so sharp Young later apologized from the bench. 

Elsewhere, Burroughs borrowed Justice Jackson’s now viral “Calvinball” metaphor, remarking that “this is not Calvinball and there are rules.”

Judge Burroughs made clear that combatting antisemitism is “indisputably an important and worthy objective,” and antisemitism must be addressed. She credited Harvard with the steps it has taken to do so, from creating the University’s Antisemitism Task Force to new accountability procedures and clarified policies and personnel changes.

However, she went on to contradict herself by discounting some of these same tactics when she wrote that the University’s governance, hiring, and admissions “have little to do with antisemitism” in the context of rejecting the government’s demands. 

The government should not overstep here, but that framing risks overlooking how institutional structures and leadership choices set the tone for campus culture — and how governance is ultimately responsible for fostering an environment where students can learn and faculty are able to participate in Harvard’s academic mission.

Alongside Harvard, several “organizational plaintiffs” — including the American Association of University Professors (AAUP), its Harvard chapter, and unions representing graduate students and academic workers — also challenged the funding freezes and terminations.

Judge Burroughs found that AAUP — a faculty group whose Harvard chapter leaders took part in last year’s protests in the libraries — and the unions had standing to bring their claims. She granted them partial relief, unlike in the Columbia AAUP case, where a similar challenge was dismissed.

Like Harvard, the organizational plaintiffs prevailed on claims that the Freeze Orders and Termination Letters violated the First Amendment and Title VI. But because they are not direct recipients of federal research grants, their remedy is not financial restoration.

Instead, their relief is indirect: their members’ academic work and organizing benefit because Harvard’s funding is restored.

Meanwhile, several of their APA-based claims, including those tied to separation of powers and due process, remain unresolved and will continue in district court.

In short: Harvard walks away with an order restoring funding (subject to appeal), while AAUP and the unions still have active litigation in district court ahead.

April 21, 2025: Harvard filed President & Fellows of Harvard College v. HHS, challenging the freeze of more than $2.2 billion in federal research funding. The complaint argued that the freeze was:

June-July 2025: Both Harvard and the government moved for summary judgment, asking Judge Allison Burroughs to resolve the case without trial.

Late July 2025: Judge Burroughs held a hearing on summary judgment for the parties to argue their respective sides, and they have been awaiting her ruling since. 

Free speech (First Amendment): Burroughs held that the government froze funding as unconstitutional retaliation for Harvard’s protected speech and governance choices. She vacated both the Freeze Orders and Termination Letters.

Civil rights law (Title VI): She ruled the government exceeded its authority under Title VI by skipping the mandatory steps (notice, resolution attempts, hearing, Congressional notice).

Agency rules: She also said the agencies failed to follow their own regulations when imposing the freeze.

Burroughs rejected a duplicate version of Harvard’s free-speech claim, saying it was already covered by her First Amendment ruling.

She also denied Harvard’s broad claim that the executive branch never had authority to act at all, calling it unnecessary since she already struck the freezes and terminations on other grounds.

On Harvard’s claim that the freeze was “arbitrary and capricious,” Burroughs split the difference. She agreed the Freeze Orders fit that description, but said she couldn’t review the Termination Letters for arbitrariness because of the Supreme Court’s NIH v. APHA ruling.

Even so, she vacated the Freeze Orders and Termination Letters on other grounds (free speech and Title VI).

In August 2025, the Supreme Court issued a ruling in NIH v. APHA over whether and which courts can reinstate canceled federal research grants. 

The fractured opinions among the bench left Justice Amy Coney Barrett’s concurrence as the controlling one. Under her ruling, repayment claims (restoring past grant money) must go to the CFC, a specialized Washington D.C.-based court; forward-looking challenges to agency policies or constitutional violations can proceed in federal district court.

That framework now governs Harvard’s case. Judge Burroughs acknowledged it, and said she lacked jurisdiction to review the Termination Letters under the APA’s “arbitrary and capricious” standard since that looks like a repayment dispute. 

But Burroughs distinguished Harvard’s case from APHA as principally about unlawful directives, as well as constitutional statutory violations. First Amendment claims are not “money-mandating,” and Title VI expressly provides for Article III court (i.e., federal court) review.

​​On that basis, she vacated both the Freeze Orders and the Termination Letters. She emphasized that unlike APHA, where the district court could split guidance and termination into separate orders, Harvard’s constitutional and statutory claims “rise and fall together.” Therefore, they must be resolved in a single order.

The AAUP, its Harvard chapter, and unions representing Harvard’s graduate students and academic workers filed a parallel lawsuit against the same federal agencies that targeted Harvard. They argued that the freezes and terminations harmed their members directly by chilling speech, disrupting research, and undermining faculty and graduate student advocacy.

Like Harvard, AAUP also moved for summary judgment, and Judge Burroughs heard both cases together at the July hearing, since AAUP’s monetary relief ultimately depended on whether Harvard’s funding was restored.

Even so, AAUP has stressed that its interests aren’t identical to Harvard’s. Even if Harvard regains its funding, that alone doesn’t remedy what AAUP described as government “coercion” or the long-term impact on its members’ academic freedom and careers. The group also expressed concern that Harvard might settle with the government or agree to structural changes (including ones Harvard had already made) that could still leave its members exposed.

The government has already said it will appeal, sending the case to the First Circuit and, potentially, the Supreme Court. For now, Judge Burroughs’s order means Harvard’s funding should be restored unless the government secures a stay pending appeal. As President Emeritus Larry Summers wrote, “this was a good day for Harvard—and an even better day for American democracy.” 

Parallel to the courtroom fight, settlement talks remain on the table. Figures as high as $1 billion have circulated, though $500 million has been the most frequently cited. As the New York Times reports, Harvard officials have hoped that a legal victory would allow them to frame any deal with the White House “as part of a surrender by the administration.” Burroughs’s ruling may also put pressure on the government if it prefers not to fight all the way up the appellate ladder.

At the same time, the White House insisted after the ruling that Harvard remained ineligible for grants in the future. Even if Harvard regains its full $3.2 billion, the larger unresolved question is whether it will be allowed access to federal research funding in the years ahead, and if there is any way to actually stop the government from shutting Harvard out.

Finally, while Burroughs’ ruling has vacated the Freeze Orders and Termination Letters as unconstitutional and unlawful, her order does not prevent the government from pursuing future Title VI claims through proper channels and procedures. HHS’s Office for Civil Rights has already issued Harvard a Notice of Violation, and enforcement of that finding continues on a parallel track.