Higher Education Association Lawsuits Challenge NIH and DOE Cuts to F&A Reimbursement

Nationwide Temporary Restraining Order Issued in DOE Lawsuit

April 16, 2025

UPDATE: U.S. District Judge Allison Burroughs issued a temporary restraining order (TRO) that covers all institutions in all states nationwide in the case filed by AAU, ACE, APLU, and nine impacted higher education institutions against the U.S. Department of Energy. The judge’s order prevents the administration “…from implementing, instituting, maintaining, or giving effect to the DOE Policy Flash: Adjusting Department of Energy Grant Policy for Institutions of Higher Education (IHE) (the ‘Rate Cap Policy’) in any form; from otherwise modifying negotiated indirect cost rates except as permitted by statute and by the regulations of the Office of Management and Budget; and from terminating any grants pursuant to the Rate Cap Policy or based on a grantee’s refusal to accept an indirect cost rate less than their negotiated rate.”

Higher Education Groups File New Lawsuit as Administration Escalates Attack on Research Funding

April 14, 2025

Just days after securing a nationwide permanent injunction blocking the Trump administration’s attempt to cap indirect cost (F&A) reimbursements for National Institutes of Health (NIH) research, a coalition of higher education groups has filed a new lawsuit—this time challenging similar cuts imposed on Department of Energy (DOE) research grants.

The lawsuit, filed by the American Council on Education (ACE), the Association of American Universities (AAU), the Association of Public and Land-grant Universities (APLU), and a number of leading research institutions, seeks to halt the DOE’s plan to cap F&A reimbursements at 15 percent. Like the earlier NIH cap, the DOE policy was announced without warning or consultation and would dramatically undermine American research and innovation.

“These actions are part of a continuing and dangerous effort to erode federal support for university-based research,” the groups said in a joint statement. “The proposed DOE cap would have an immediate and damaging impact on critical energy, physical sciences, and engineering research at more than 300 colleges and universities nationwide.”

The suit argues that the DOE action mirrors the NIH policy already found unlawful by a federal judge—and again violates long-established regulatory frameworks and administrative law. Research funded by the DOE supports national security, energy independence, and American industrial competitiveness. Slashing the indirect cost rate jeopardizes not only the research itself, but also the infrastructure and training pipelines that make it possible.

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Federal Court Issues Permanent Injunction Against NIH Cap on University Research Reimbursements

April 7, 2025

The federal district court on Friday, April 4, 2025, converted the exiting preliminary injunction into a permanent one, that halts the implementation, application, or enforcement of the National Institutes of Health’s Feb. 7 supplemental guidance imposing a cap of 15 percent on facilities and administration (F&A) costs reimbursement to universities who receive NIH research grants.

The order entered Friday was the product of a joint motion from the plaintiffs, including the Association of American Universities, the American Council on Education, the Association of Public and Land-grant Universities, twelve higher education institutions, the Association of American Medical Colleges, and 22 states’ attorneys general. The court’s permanent injunction continues to apply to all institutions nationwide. The government is expected to appeal the ruling to the U.S. Court of Appeals for the First Circuit.

Nationwide Preliminary Injunction Granted in NIH Lawsuit

March 5, 2025

Judge Angel Kelley of the United States District Court for the District of Massachusetts today issued a preliminary injunction halting the implementation, application, or enforcement of the National Institutes of Health’s Feb. 7 supplemental guidance imposing a cap of 15 percent on facilities and administration (F&A) costs reimbursement to universities who receive NIH research grants. The injunction applies to all institutions nationwide. This preliminary injunction replaces the temporary restraining order that had been in place since February 11, which also halted the implementation of the supplemental guidance.

While a temporary restraining order is put in place when a court determines that plaintiffs have provided enough evidence to show that irreparable harm is likely to result if an action is not halted temporarily, a preliminary injunction requires a higher standard of review. The ruling means that the judge has considered not only the harms that the enjoined action is likely to cause, but also the potential merits of the underlying case. The ruling means that the NIH’s action is halted until the judge renders a final decision in the case or the defendants successfully get a higher court to overturn the injunction, whichever comes first.

The injunction follows a hearing held on Feb. 21, 2025, during which both the representatives from separate lawsuits as well as the government presented arguments concerning the motion for preliminary injunction. The three lawsuits were filed by AAU, APLU, ACE, 12 member universities, and one university system; the Association of American Medical Colleges; and 22 state attorneys general. The government is expected to appeal the decision.

Lawsuit Challenges NIH on F&A Reimbursement

February 10, 2025

ACE, the Association of American Universities (AAU), and the Association of Public and Land-grant Universities (APLU), along with several research universities, have filed a legal challenge against the administration’s decision to cap Facilities and Administrative (F&A) reimbursements at 15 percent for NIH research grants. The lawsuit, filed in the U.S. District Court for the District of Massachusetts, seeks to halt the proposed cuts, arguing they violate established federal grant regulations and administrative law.

February 12, 2025

On Feb. 11, Judge Angel Kelley confirmed that the motion by ACE-AAU-APLU for a temporary restraining order (TRO) need not be granted because her TRO granted earlier in the day in a similar Association of American Medical Colleges (AAMC) lawsuit covers all institutions in all states nationwide. The three associations are heartened that the NIH research F&A cut is fully blocked from implementation under that order. A hearing in the ACE-AAU-APLU case, the AAMC case, and the Attorneys’ General suit has been set for next Friday, February 21 regarding an extension of the emergency TRO and next steps for progressing to the injunction phase of litigation. The case will be represented by lead counsel Paul Clement from Clement & Murphy, along with Jenner & Block.

February 21, 2025

On Feb. 21, Judge Angel Kelley extended the nationwide hold on the Trump administration’s plan to cap F&A reimbursements. This decision keeps the temporary restraining order (TRO) issues on Feb. 11 in place while the court considers whether to convert the TRO into a preliminary injunction (which would stay in place until the conclusion of the lawsuit, or unless an appeals court dissolves it).