WASHINGTON, D.C. -- Soon after the Trump administration announced it was cutting billions of dollars in grants to Harvard University following a breakdown in discussions over antisemitism on campus, the Ivy League institution pulled out the biggest weapon in the federal legal arsenal: the First Amendment.

“The Government’s attempt to coerce and control Harvard disregards … fundamental First Amendment principles,” Harvard’s lawsuit says.

But while citing the Bill of Rights’ best-known guarantee is an attention-grabber – both for judges and the general public – a more arcane issue is the focus of many of the lawsuit’s 51 pages: Harvard’s claim Trump’s executive branch isn’t following federal rules for changing key government policies.

In particular, the Administrative Procedure Act “requires this Court to hold unlawful and set aside any final agency action that is ‘arbitrary, capricious, an abuse of discretion, or otherwise not in accordance with law,’” Harvard says in its lawsuit.

It was only hours after its talks with Harvard fell apart that the White House froze $2.2 billion fueling much of the school’s research, a breakneck response that mirrors the pace of sweeping changes on issues from immigration and tariff policy to federalstaffing by an administration that prefers quick, unilateral action to deliberation and compromise.

“No administration has done anything like this before precisely because there are procedures in place to restrain this kind of extreme thing,” David A. Super, a professor of administrative and constitutional law at Georgetown and Yale, told CNN.

Whether the government can impose broad demands on Harvard as a precondition for funding appears to be the latest Trump controversy inevitably headed for the Supreme Court. And while predicting what the high court will do is usually a fool’s errand, Georgetown Law professor Steve Vladeck believes Harvard’s case is strong.

“It’s not that controversial a proposition that the government’s not allowed to say in exchange for this money – which we’re going to give you to fund medical research, to fund new scientific methods, etc. – you have to only teach the classes we tell you to teach or you have to only hire the administrators we tell you to hire,” the CNN contributor told the network’s Laura Coates on Monday.

Why the Administrative Procedure Act could be key in court

The Administrative Procedure Act, known as APA, was passed in the wake of World War II, as the government struggled to manage the major expansion of federal agencies under President Franklin D. Roosevelt.

“Congress passed the APA to guard against irrational, emotional, unfounded decision-making,” Super said. “Its purpose is not to push any particular agenda substantively but to make sure that the executive branch is following the law and considering the facts before it acts.”

The APA does not require a hearing for every decision made by a government agency, but it does say agencies should not suddenly change procedures without reason.

Harvard argues suspending federal medical and scientific research funding as a way to combat antisemitism doesn’t make any sense and upends official procedures they had come to expect with no warning.

“For decades, Harvard has relied on the well-established process for federal financial assistance in its budgeting and financial planning, including with respect to staffing, infrastructure, facility and equipment purchases, and long-term investment decisions,” the university said in its suit.

While the Trump administration asserts Harvard has allowed antisemitism to flourish in violation of the Civil Rights Act, the university says it is already addressing concerns from Jewish students and faculty by tightening its ban on encampments and other protests that disrupt student activities, making “doxing” a violation of its anti-harassment and anti-bullying rules and expanding “inclusion and belonging efforts” to include Jewish students.

Further, Harvard says the Civil Rights Act requires the government to first give it a chance to fix any violations before taking federal money away.

“Agencies have to follow their own procedures. If they say they’re going to give you a warning, they have to give you a warning,” Super said. “They can’t say, ‘Well, we’re mad, so we’re going to bypass the warning.’”

In its lawsuit, Harvard argues the Trump administration did just that: “They issued a Freeze Order on research funding first (with no process or opportunity for voluntary compliance) and used that freeze as leverage to negotiate,” Harvard’s attorneys wrote. “Such action is flatly unlawful and contrary to statutory authority.”

Indeed, the university learned the billions in federal funding would be frozen at the same time everyone else did – in the final 26 words of a one-page news release from the government’s Task Force to Combat Anti-Semitism, it says. The release was issued on the same day Harvard President Alan Garber announced the school would not agree to the administration’s demand letter.

The Trump administration’s attorneys have not yet provided a response to the allegations in the lawsuit, but White House Press Secretary Karoline Leavitt said Tuesday, “The president has made it quite clear that it’s Harvard who has put themselves in the position to lose their own funding by not obeying federal law, and we expect all colleges and universities who are receiving taxpayer funds to abide by federal law.”

Harvard’s decision to challenge the funding freeze in court seemed to take the administration by surprise. One White House official considered the back-and-forth with Harvard all part of a negotiation, they told CNN, and Education Secretary Linda McMahon said in a CNBC interview, “We would like to be able to move forward with them and other universities.”

But along with the carrot, the White House official continued to brandish a stick at Harvard.

“They want to remain the envy of the world when it comes to research and science and academia, and they can only do that if they work with this administration,” the official told CNN.

SCOTUS likely will be final word on APA limits

Harvard is far from the only group affected by the Trump administration’s orders to mention the APA when fighting back in court. More than 160 lawsuits have cited alleged violations of it, from complaints over international students facing deportation and fired federal workers to transgender students’ access to sports.

Lawsuits challenging the finer points of federal law often take years to resolve, but Harvard is asking a judge to speed up the process, saying time is of the essence to avoid harm to their programs.

“While Harvard is diligently seeking to mitigate the effects of these funding cuts, critical research efforts will be scaled back or even terminated,” the university’s lawyers wrote Wednesday in a court filing asking for an expedited hearing.

With so many lawsuits pending, the question of how much the APA can limit the White House is almost certain to be decided by the Supreme Court. An early ruling from the justices indicated that, despite showing sympathy to APA-based challenges in the past, citing that law is not a guarantee of success.

Earlier this month, they blocked a lower court’s order to delay the Trump administration’s planned termination of $600 million in teacher training grants to states, saying the APA does not necessarily give courts the power to force the government to pay grant money.

“The Government is likely to succeed in showing the District Court lacked jurisdiction to order the payment of money under the APA,” said the unsigned order from the conservative majority.

It was a 5-4 ruling, with conservative Chief Justice John Roberts siding with the court’s three liberal justices, a split that makes future decisions in similar cases even more difficult to predict.

The issue at the heart of the teacher grants case – with states arguing withholding grant money over diversity, equity and inclusion policy amounted to a broken promise from the government rather than a First Amendment dispute – is different than Harvard’s.
But it shows the rocky road anyone challenging the White House’s administrative decisions could face, perhaps including Columbia University, which cut its own deal last month over federal funding tied to policy demands over antisemitism.

Still, education advocates say, it’s worth facing the legal uncertainty to draw a line in the sand.

“Harvard did absolutely the right thing. They came up with a very courageous decision, and more importantly, I think, they made great arguments for why this kind of federal overreach is beyond the pale,” said American Council on Education President Ted Mitchell.

And the extreme speed of the actions of taken against Harvard – the unapologetic pace Trump prizes – is likely to be the government’s legal undoing, Super said he believes.

“These actions are so sloppy that I don’t see any serious chance that they’ll survive,” he said.

CNN’s Katelyn Polantz, Tierney Sneed and Betsy Klein contributed to this report.

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