What legal rulings have been issued so far in the lawsuits challenging the Trump administration’s NIH funding actions?
Executive summary
A string of federal rulings has both checked and allowed parts of the Trump administration’s effort to rework National Institutes of Health funding: a federal district court found mass terminations of grants unlawful and ordered reinstatements, the Supreme Court temporarily allowed the administration to stop paying hundreds of millions tied to DEI-linked grants while leaving other parts of lower-court orders intact, and the First Circuit has affirmed a permanent injunction blocking a separate effort to impose sweeping caps on NIH overhead reimbursement rates [1] [2] [3]. Separate settlements and agreements require NIH to re-review thousands of frozen or denied applications under the agency’s usual processes, though many terminated awards remain unresolved [4] [5] [6].
1. District court: terminations ruled “void and illegal,” reinstatements ordered
In June a federal trial judge in Boston, District Judge William G. Young, concluded that the administration’s directive terminating hundreds of existing NIH grants was arbitrary, capricious, and unlawful, describing portions of the policy as discriminatory and ordering some grants restored [1] [5] [7]. That decision addressed the legality of canceling already-awarded projects—finding the agency had failed to follow required evaluation procedures before cutting funds—and formed the backbone of plaintiffs’ contention that agency directives violated both process and statutory constraints [7] [1].
2. Supreme Court intervention: partial stay on payments but not on other rulings
The Supreme Court stepped into the litigation later, issuing an order that effectively allowed the government to halt payment on roughly $783 million in grants tied to diversity, equity and inclusion (DEI) initiatives by a 5–4 vote while leaving intact other parts of the lower court’s findings [2]. The high court’s brief order relied on jurisdictional reasoning and a concern about irreparable harm to the government if required payments proved unrecoverable, narrowing the district court’s remedial reach even as it left open questions about agency internal guidance and policy documents [2] [5].
3. First Circuit: blocks broad overhead-cut policy, affirms permanent injunction
Separately, a coalition including 22 state attorneys general and major university and medical groups secured an injunction against NIH guidance that sought to cap indirect cost reimbursements; that preliminary block was affirmed on appeal when the First U.S. Circuit Court of Appeals held the policy violated NIH regulations and statutory language designed to protect negotiated indirect cost rates [3] [8] [9]. The appeals panel agreed with U.S. District Judge Angel Kelley’s earlier ruling and converted earlier relief into a permanent injunction, a decision heralded by state AGs as preventing “decimation” of research funding [3] [10] [11].
4. Settlement and review commitments: hundreds to thousands of applications to be re-examined
Amid litigation over future and pending applications, the government reached agreements requiring NIH to re-review hundreds—or by some counts thousands—of grant applications that had been frozen, denied, or withdrawn after the February directive, committing the agency to use its “usual process” and evaluate proposals in good faith without conceding liability [4] [5] [6]. The settlements do not guarantee funding and explicitly leave nearly 850 terminated grants outside the re-review settlement; the government has also preserved its appellate rights on other rulings [6] [4].
5. Competing narratives and legal posture going forward
The court records and press statements reveal competing frames: plaintiffs emphasize procedural violations and potential discrimination in cutting grants, while administration spokespeople defended policy changes as restoring scientific rigor and reallocating resources; the government has continued appeals, and the Supreme Court’s partial stays produced a mixed legal landscape that leaves some remedies intact while allowing the administration to avoid immediate payment on large sums [1] [2] [4]. Reporting and official releases indicate that multiple cases—some consolidated, some split into phases addressing terminations versus application processing—remain in play, so the legal picture is fragmented and evolving as appellate briefing and compliance with settlement terms proceed [5] [7].
6. What the rulings mean in practice and what remains unresolved
Practically, the combined rulings and settlements have prevented the administration from unilaterally imposing a uniform cap on overhead reimbursement and have forced NIH to re-evaluate delayed applications under ordinary review procedures, but they have not fully reinstated all terminated awards because of the Supreme Court’s intervention and separate unresolved appeals; large questions remain about which specific projects will ultimately receive funding and how long reviews will take [3] [6] [2]. Coverage and official statements reflect ongoing tension between judicial checks on agency rulemaking and the administration’s assertion of policy prerogatives, and the litigation’s next chapters will hinge on appellate decisions and the practical outcomes of the mandated re-reviews [9] [4].