For some college students, the Covid vaccine is a price they are not willing to pay for a degree.

Justin Mishler, a 29-year-old junior at Northern Illinois University, is one of them. After serving in the U.S. Marine Corps, Mishler enrolled in the state school in 2016 through the GI Bill, which helps cover the cost of tuition, books and housing.

During the pandemic, he took time off to work rather than attend school remotely.

This fall, Mishler would have returned in person, but, in August, Northern Illinois announced all students must submit proof of vaccination or request an exemption and get tested weekly.

“I was excited but when I saw you had to be vaccinated, I decided to keep working instead,” he said.

More from Personal Finance:
How to maximize your college financial aid
Many companies are offering tuition assistance
College plans rebound although cost is a top concern

“I’m not going to abide by stuff I don’t believe in.”

For now, Mishler drives a forklift at a nearby 3M facility in DeKalb, Illinois.

“I would like to be able to finish [my degree] and work in a military museum,” the history major said. “But if it never goes back to normal, I’m just going to do something else.”

Dylan Dean, 22, preemptively unenrolled from Montana State University — even before MSU finalized a Covid policy. “I was worried there would be mandates,” he said.

Although Dean, a senior majoring in electrical engineering, will no longer graduate in the spring, he said he “had no faith” that the university would not institute a vaccine mandate if he returned to campus this fall.

“I think vaccine mandates fail to take into account natural immunity,” Dean said.

At MSU, students are not required to get vaccinated for Covid-19. Rather, the university encourages vaccinations by holding weekly drawings for vaccinated students with prizes such as $5,000 financial aid awards, a season ski pass, airline vouchers or even a hot-air balloon ride.

On Sept. 17, the university did expand its guidance on face masks after the Bozeman hospital’s critical care unit reached 100% capacity. Masks, which were only mandatory in class, and are now required in other indoor areas, as well, including the library, residence halls and dining facilities on the Bozeman campus.

“These precautionary measures are necessary to protect each other and to keep in-person classes and events on the campus we love,” MSU’s President Waded Cruzado said in a letter to the community.

Dean says parents supported his move to withdraw from the fall semester. “They don’t agree with me politically, but they know this is my decision.” Dean is a member of Young Americans for Liberty, a libertarian group active on nearly 400 college and university campuses.

Altogether, roughly 1,000 colleges and universities across the country are requiring vaccines for at least some students or employees, according to data compiled by the Chronicle of Higher Education. In most cases, students who refused to get vaccinated weren’t able to register for classes or had their enrollment revoked.

Some are petitioning, others are taking their cases to court. Already, there have been dozens of lawsuits challenging school vaccination requirements. Yet no college has reversed its policy.

Over the summer, a federal judge upheld Indiana University’s Covid vaccine requirement for the fall semester, dealing another blow to students who disagree with vaccine mandates. ”This university policy isn’t forced vaccination,” the judge said. There are other options, including “taking a semester off, or attending another university.”

Cases against the University of Massachusetts and the University of Connecticut were also dismissed in federal court. More are pending.

Covid outbreaks on college campuses have the potential to derail the fall semester, as well as the entire higher education system, according to Lynn Pasquerella, president of the Association of American Colleges and Universities.

Last year, sudden spikes in coronavirus cases among undergraduates caused many schools to reluctantly return to remote instruction even though students overwhelmingly declared virtual learning an inadequate substitute for being in the classroom.

In the end, a significant number of students opted out entirely.

Subscribe to CNBC on YouTube.