President Trump’s $100,000 fee for new H-1B visas will have major consequences for tech companies and financial firms. But the effects of the new fee will also ripple across the education system and show up in classrooms across the country.

Higher education leaders and public-school superintendents say the steep fee will hurt schools that depend on foreign workers to fill critical teaching roles. Some university and college presidents said it would impede their ability to hire faculty members through the visa program, which allows educated foreign citizens to work in “specialty occupations.” Others said their school districts could not afford the fee, making it harder for them to find math and special education teachers.

The change is yet another blow to colleges and universities that have been squeezed by the Trump administration’s barrage of attacks on higher education. Federal officials have frozen billions in research funds, demanded hefty payments from top schools, intensified vetting of student visas and pursued civil rights investigations into dozens of universities.

Administration officials say the H-1B visa program lets employers sideline American workers and suppress their wages. They have argued that the new fee will help counter that by encouraging employers to prioritize hiring domestic workers.

But some education leaders said they worried the change would make institutions less competitive and restrict their ability to hire the best candidates.

“It’s not as if this is done on a whim because we’re trying to replace American workers,” said Lynn Pasquerella, the president of the American Association of Colleges and Universities. “It is done based on what the Trump administration is calling for — on merit and who’s the most qualified.”

Dr. Pasquerella said many schools depended on the visas to fill positions in the STEM and medical fields. She said she was particularly concerned that the pipeline for foreign physicians would be further constrained.

Although she said that not all STEM fields faced worker shortages, there was still a need in areas like nuclear engineering and material science. She said the new fee would also hurt universities’ ability to innovate and make advancements in fields like artificial intelligence because “global collaboration is being undermined.”

Tech companies are among the biggest users of H-1B visas. The professional, scientific and technical services sector accounted for nearly half of all approved petitions for H-1B workers in the 2024 fiscal year, according to data from U.S. Citizenship and Immigration Services. Educational services made up about 7 percent, a smaller but sizable amount.

Stanford University, the University of Michigan, the University of Maryland and the University of Pennsylvania are among the institutions that have had the most H-1B visas approved in recent years.

Some university leaders said the policy change would impede their ability to hire as many employees who need skilled-worker visas.

“It will depend upon the subject-area expertise,” said Dr. Jeffrey P. Gold, the president of the University of Nebraska system. “But if we had to absorb this cost, it will definitely reduce our ability to hire individuals with H-1B visas.”

About 500 employees in the system currently have H-1B visas, Dr. Gold said. Although that is a small number compared with the university’s total work force of roughly 16,000, many of those workers fill important positions in the technology and precision agriculture field, he said. Some also work as physicians or professors at the university’s medical center.

The new fee could result in leaving some positions unfilled, cutting expenses in other areas or passing on higher costs to students, Dr. Gold said. Although the university always prioritizes hiring domestic workers, he said, it can be difficult to find enough qualified workers to fill certain roles.

Dr. Gold said those employees also helped “enrich the environment,” bringing unique knowledge and experience from around the world. And if the university cannot fill jobs in health care, that could lead to longer appointment times and delayed care, he said.

Andrew Martin, the chancellor of Washington University in St. Louis, said that the university sponsored around 285 new H-1B visas each year and that officials there were “in the trying-to-figure-it-out phase.”

“In a world in which we’re on the hook for $100,000 for each of these visas, we’re going to have to think very, very carefully about our hiring practices,” Dr. Martin said. “Most of these positions aren’t positions for which we can hire domestically,” he said, pointing to, for example, America’s shortage of anesthesiologists.

Dr. Martin also said the shift threatened to affect the attractiveness of the United States for international students who might enroll with hopes of remaining in the country after graduation.

Some smaller colleges said they would have to quit hiring new workers through the visa program entirely.

Elizabeth Kiss, the president of Union College in Schenectady, N.Y., said the college employed 16 faculty members with H-1B visas who worked across nine departments. But she said the college could not afford to hire people through the program anymore.

“We are absolutely not in a position in the future to pay the $100,000 fee,” Dr. Kiss said, adding that it was a tenfold increase compared with the amount the college had been paying for each visa before.

The impacts of the new fee will also extend to local school districts. Tara Thomas, the senior government affairs manager at AASA, the School Superintendents Association, said districts across the country had relied on H-1B visas to fill vacancies as staffing shortages continued.

“Adding this fee will basically eliminate this as an option for districts,” Ms. Thomas said. “I just don’t see how any district could make it work.”

Wendy Birhanzel, the superintendent of Harrison School District 2 in Colorado Springs, said her district employed seven teachers with H-1B visas. Although she said the district tried to hire American workers, it was challenging to find qualified candidates to fill math, science and special education roles. As a result, the district started to hire more foreign-born workers — mostly from the Philippines, Mexico and India — about a decade ago. She added that those employees were “on the same teacher pay scale as an American worker.”

The district wants to keep one math and two special education teachers who are currently working on J-1 visas that will expire soon, Dr. Birhanzel said, but it cannot afford the steeper fees for them to obtain H-1B visas to stay longer. The $100,000 fee is substantially higher than the roughly $7,000 it usually costs for each visa, she said.

Dr. Birhanzel said the district would probably have to rely on long-term substitute teachers or increase class sizes if it lost those teachers and could not fill their positions. That could affect student learning because substitute teachers might lack experience in the fields they teach in, she said.

“You could have someone who got a bachelor’s degree in music teaching calculus,” Dr. Birhanzel said. “We would put teachers with no special education expertise with our most vulnerable learners.”

Dr. Birhanzel said she hoped to see the Trump administration provide an exemption for school districts.

The administration has provided few details about which jobs would qualify for an exemption. According to the proclamation Mr. Trump signed, the homeland security secretary can deem certain positions exempt if hiring those foreign-born workers is “in the national interest.”

Sophie Alcorn, an immigration lawyer in Silicon Valley, said several universities she advises had paused filing new H-1B visa applications if roles did not need to be urgently filled, in large part because there had been confusion over how employers can apply for a national-interest exemption or submit payments to cover the fee.

“They’re all taking a comprehensive look at their hiring strategies,” Ms. Alcorn said. “A $100,000 fee for an educational nonprofit institution is definitely not in the budget this year as the budget has already, in general, been decreasing due to other factors, such as the reduction in grants and international student enrollment.”

Some university leaders have also questioned whether they will be subject to the new fee, given that higher education institutions are generally exempt from the 85,000 annual cap for H-1B visas. A White House official said the $100,000 fee did apply to any cap-exempt petition filed after Sept. 21.

Some policy experts said they were encouraged by the administration’s changes. Elizabeth Jacobs, the director of regulatory affairs and policy at the Center for Immigration Studies, a think tank that favors restricting immigration, said the new fee would help ensure that employers had a “legitimate need” when they sought H-1B visas.

“I do think it’s a positive change from the status quo,” she said. “However, I think we do need more information about how this will be implemented.”

She said she did not see a compelling reason to give universities an exemption, and she thought it was important that they preserved room for hiring U.S. citizens and green card holders for highly coveted research positions.

But some college leaders emphasized that they considered the quality of people’s work. Leon Botstein, the president of Bard College in the Hudson Valley, which employs more than two dozen employees with H-1B visas, said the college would be “forced to reconsider getting the best people if they came from abroad.”

“It’s not patriotic,” Dr. Botstein said. “It harms the economy and has nothing to do with excellence.”

Alan Blinder contributed reporting.