“Its finances are just stretched very thin compared to its mission,” said Larry Ladd, a higher education finance and governance expert with the Association of Governing Boards of Universities and Colleges.

Graduate student enrollment has nose-dived, the university’s national ranking, which helps it attract international students who pay full tuition, has dropped precipitously, and, as of this semester, undergraduate enrollment has slipped.

The financial pressure led to a mass layoff in the summer, hiring freezes and spending cuts, a halt in plans for a new science facility, an unusually large drawdown from the endowment to subsidize operations, and, for the first time in a decade, a budget deficit and a cash loss at the end of the past academic year.

Morale among students and faculty has taken a hit. “Brandeis, we are so embarrassed” was the headline of an editorial in the student newspaper last month about the financial struggles. Then, on Sept. 25, following a faculty no-confidence vote that cited, among other complaints, the school’s financial woes, president Ronald Liebowitz resigned effective Nov. 1.

“I have done so with mixed emotions because this is an exceptional institution,” he said in a statement.

The financial challenges are not unique to Brandeis. Schools across the country are contending with declining enrollment, ballooning expenses, and frenzied competition to attract students with new dormitories, cafeterias, and other costly amenities. Many are now financially stressed and some small liberal arts colleges have closed.

Selective universities, such as Brandeis, have been less susceptible to the wider malaise in higher education. But Brandeis is singular. It was founded in 1948 by the American Jewish community to serve Jews and other groups who faced discrimination in higher education. And although it is relatively small, Brandeis is a major research institution, where four faculty or alumni have won a Nobel Prize since 2003.

But its younger age, size, and research focus make it vulnerable: It does not have generations of alumni donors like Ivy League schools. Unlike many other major research institutions, it has fewer than 5,500 students, not the tens of thousands of tuition-paying students other schools can rely on to defray costs.

“We all know we have higher education headwinds. We have particular headwinds at Brandeis,” Liebowitz said in April.

Those headwinds grew especially stiff during the past academic year.

In a confidential presentation in May seen by the Globe, chief financial officer Samuel Solomon said the “[b]iggest driver of underperformance” was a decline in tuition revenue from graduate students, down 46 percent since 2019.

Undergraduate enrollment, which is a much bigger source of revenue, had been stable — until the fall. The new first-year class came in about 100 students short of the annual target of 900. That has raised concerns among Brandeis leaders that undergraduate revenue could erode, as well.

“The problem is that’s a shortfall from one class that carries over each year, and if we continue to have class shortfalls that number grows,” said a senior Brandeis administrator, who requested anonymity because they were not authorized to speak.

The shortfall occurred after an academic year when Liebowitz and Brandeis’s board advertised the school as a refuge for Jewish students concerned about campus antisemitism in the wake of the Israel-Hamas war. The board backed Liebowitz as he voiced a pro-Israel stance and took a hard line on elements of pro-Palestinian activism he saw as antisemitic.

Ulka Anjaria, a Brandeis English professor, said faculty morale has taken a hit because of a perception that students are less interested in attending Brandeis than they once were. The school’s drop in the U.S. News and World Report rankings, from a peak of 35th in 2019 to 63rd in the most recent edition, hasn’t helped. Part of the dip was caused by a change in the scoring rubric that generally helped large, public universities and hurt schools like Brandeis that prioritize small class sizes.

“The rankings are not unproblematic. We certainly don’t abide by them,” Anjaria said. But it has been dispiriting, she said, to see universities that Brandeis considers its peers, such as Northeastern and Tufts, pull ahead. And a lower ranking can take a toll on revenue by dissuading students from attending.

Brandeis leaders say the current financial difficulties are part of a normal ebb-and-flow and not indicative of a decline.

The smaller first-year class comes after recent classes exceeded the 900-student target. So, overall, the undergraduate student body is 40 students short, or 1 percent, said Stewart Uretsky, Brandeis’s executive vice president of finance and administration.

The cash loss of $8 million for the 2024 fiscal year, he said, was “largely attributable to costs associated with starting the preliminary design work on two buildings.” One of those projects was the science facility, which is “temporarily paused” but “will restart,” he said. The other is a planned 650-bed dormitory.

The budget deficit, which is calculated differently, was $1.7 million on a total budget of more than $400 million.

“We are similar to many nonprofit institutions that generate a relatively narrow operating margin,” Uretsky said. Although it was “slightly negative” for the 2024 fiscal year, which ended in June, “it had been slightly positive for the nine prior years,” he said.

But Brandeis’s needs are much greater than what the current deficit reflects. Internally, leaders have concluded they should spend tens of millions more on salaries, facilities, and maintenance, and draw less from its endowment, just to remain competitive — but cannot afford to do so. “Our financial problems are an order of magnitude worse,” said the administrator, who has access to the school’s financials.

Uretsky said, “Any imbalance in our finances . . . indicates we are an ambitious institution filled with faculty, staff, and students who strive to advance knowledge, and we must make responsible choices to operate within our means.”

For the 2025 fiscal year, the university is spending 7 percent of the value of its $1.2 billion endowment. Nonprofits generally aim to spend less than 5 percent of their endowment per year. Uretsky said the 7 percent draw is “on the high end of an acceptable range, not outside of it.”

The editorial board of The Justice, the student newspaper, has said that Brandeis’s buildings, many dating to the mid-century, are “crumbling.” Emergency repairs are common, the board wrote.

Since 2016, Brandeis has increased its capital budget 50 percent, Uretsky said.

Liebowitz, the outgoing president, said in April that throughout Brandeis’s 76 years, “everything was reinvested into the academic program, rightly so. . . . The university has done a remarkable job of investing and reinvesting in that research endeavor. But ultimately, eventually, that’s at the expense of what other investments weren’t [made]. So you look at the campus infrastructure and we don’t have the amenities.”

“Those are the challenges for Brandeis: to remain academically excellent and also competitive with all the other desires of this particular generation,” he said.

Hilary Burns of the Globe staff contributed to this report.

Mike Damiano can be reached at mike.damiano@globe.com.