NEW YORK — The quiet of the summer seemed a good time for at least one new enrollee to come fill out his paperwork for the master’s program in public administration at Baruch College, part of the City University of New York.

Except for the backpack he was wearing, it would have been hard to pick him out as a graduate student. Like many Americans who go to graduate school, he works full time and will attend Baruch part time for the next three years in hopes of improving his career prospects. He’ll pay for it himself with student loans.

That’s why he was so perturbed to learn that, on top of the tuition he has already budgeted for, he’ll have to pay the university a $1,000-a-year “academic excellence fee.” He’s lucky it’s only that much. In one department at Baruch, this fee is $2,000 a year; in another, $8,000.

The student, who spoke on the condition of anonymity because of fear of retribution from administrators for discussing it, said he didn’t plan for that additional cost.

“This is not cheap,” he said outside the university’s Information and Technology Building.

“It’s like when you’re an undergraduate,” he said, rattling off all the fees he paid then. “Technology fee. Transportation fee. Student activity fee. There’s, like, five other fees that all have weird names. You’re already paying for these services. It’s just another way of charging extra.”

If undergraduates are tired of these fees, graduate students are incensed — and are starting to push back. This is especially true among the many who were promised free tuition and small stipends to work as teaching or research assistants but have been surprised to find they have to pay thousands of dollars in fees with euphemistic names and indeterminate purposes. Some of these students, who help teach undergrads and supply labor in campus labs, are taking out loans just to pay the fees.

And although there remains reluctance among graduate students like the one at Baruch to jeopardize their standing by speaking out, others are transforming their anger into strikes and protests. A handful of faculty are taking up their cause.

The total amount of fees charged by universities and colleges more than doubled in the 15 years ending in 2017, the last period for which the figure is available, even when adjusted for inflation. That’s up faster than tuition, which rose about 80 percent during that time, according to one of the few analyses of this little-reported part of college costs, by Seton Hall University education professor Robert Kelchen.

There’s no comprehensive breakdown of graduate student fees alone, but many institutions have increased them. One study of fees paid by graduate students at top research institutions found they’re $4,653 a year at Louisiana State University, $3,622 at North Carolina State University and $3,160 at the University of Tennessee.

Baruch did not initially explain, despite being asked repeatedly over five weeks, the purpose of its “academic excellence fee.” School spokeswoman Suzanne Bronski provided a statement saying that all fees are disclosed on the website and that an “overwhelming majority” of similar institutions also charge them. Bronski later said the fee paid for graduate faculty, advisers and career services.

Figures disclosed in response to a public records request show that the school collected $8.8 million from graduate student fees in the academic year just ended, on top of the $29.8 million in graduate tuition it charged.

Many fees similar to Baruch's were added during the Great Recession by public universities when state funding was cut. Instead of being phased out as the economy recovered, the fees have steadily increased.

The University System of Georgia Board of Regents imposed a “special institutional fee” of $100 a semester as a “temporary measure” to make up for state cutbacks in 2009. It’s still there, and is up to $344 a semester for graduate students, part of a slate of fees that add up to $1,012 per semester.

“It may not seem like a lot, but when you’re making [a stipend of] $25,000 and working in a major city, it’s a major problem,” said Joshua Weitz, a professor of biological sciences at the Georgia Institute of Technology.

Weitz depends on graduate teaching and research assistants, and has become a critic of these fees.

“We would expect that we wouldn’t be making them pay a fee to do the work we want them to do,” he said.

Terri Dunbar, a doctoral student and teaching fellow in psychology at Georgia Tech, estimated her fees to be about $4,000 a year, including for the summer, when she stays on campus. Unable to cover those from her $20,000-a-year stipend while living in Atlanta, Dunbar said, she has borrowed about $20,000 to pay them.

It’s not unusual for fees to suck up large proportions of the generally small stipends paid to graduate teaching and research assistants, said Jon Bomar, an officer of the National Association of Graduate-Professional Students and a doctoral candidate in biomedical engineering at the University of Maine.

“Taking another 10 or 20 percent out of that, that has a huge impact on students,” Bomar said.

Universities charge vaguely branded fees, he said, because “it’s a way to raise the cost of education without having to make that very publicly accessible.” Many graduate students don’t realize they have to pay these fees until they have accepted an appointment, because appointment offers often promise that tuition will be waived without mentioning the fees, and some university websites make a puzzle out of finding them.

“I don’t think it’s inaccurate to say they’re hidden fees,” Bomar said.

Yet as angry as they are, "a lot of grad students get scared that they'll get kicked out of their labs if they speak out" about this, Dunbar said.

That’s beginning to change.

More than 1,500 graduate teaching and research assistants at the University of Illinois at Chicago went on strike in March, partly over increases in the fees they were being charged while making wages that started at $18,000 a year. The students won a slight bump in pay and reduced fees.

Graduate students at the University of Colorado at Boulder have held repeated demonstrations against fees that come to $2,088 a year for law students and $1,732 for other graduate students. They’ve had some success, too: A task force set up in response to the protests recommended that mandatory fees be dropped for graduate students who teach and do research — over time, and assuming funding becomes available.

The University of North Carolina at Chapel Hill, where graduate students pay $2,035 a year in fees, has announced that “some, but not all” mandatory fees will be eased “in most cases,” beginning in the fall, for graduate students who also teach and do research. But that will happen only if the students’ departments decide to subsidize the fees on their behalf, or if the grants that subsidize the students’ work can be used to pay the fees. A spokeswoman said there was no way of estimating how many students would benefit, and to what extent.

The University of Colorado at Boulder graduate students said the mandatory fees they pay consume nearly 10 cents of every dollar of the $22,000-a-year stipends they receive for teaching and conducting research. “It’s pretty absurd to have to pay to do your job,” said Alex Wolf-Root, an organizer for the graduate student union.

The University of Colorado task force report gave a rare glimpse into why universities are quick to add and reluctant to reduce fees. On that campus, it said, every $13 reduction in undergraduate and graduate fees would cost $1 million.

At the University of Colorado, there’s no timeline to respond to the task force’s proposal, a spokeswoman said, which the task force estimated would cost the university an estimated $3.3 million a year.

Weitz, at Georgia Tech, said fees on graduate teaching and research assistants “may make sense as a way to raise revenues, but they create a strange disincentive and penalize a class of workers who are at the very lowest end of the salary range.”

Graduate students are “a core engine of research and discovery,” he said. “By imposing these fees, we’re limiting our talent pool.”

This story about graduate students was produced by The Hechinger Report, a nonprofit, independent news organization focused on inequality and innovation in education. Sign up for our higher education newsletter.