ATLANTA — Lia Thomas, the transgender woman whose record-threatening times on the University of Pennsylvania’s swim team made her a star of college athletics and a symbol of the debate over sports and gender identity, won an N.C.A.A. championship in the 500-yard freestyle on Thursday.

Thomas, a fifth-year senior who arrived for the swimming championships in Atlanta as the top seed in the 500 and 200 freestyle races, completed the race in 4 minutes, 33.24 seconds, more than a second ahead of the runner-up.

Thomas’s victory made her the first openly transgender woman to win an N.C.A.A. swimming title, a feat that came nearly three years after the hurdler CeCe Telfer became the first openly transgender person to capture an N.C.A.A. championship.

But Thomas’ triumph in Atlanta — indeed, her very presence at the swimming championships as a contender — came amid a far larger storm, particularly in statehouses and right-wing media, about sports participation by transgender girls and women seeking to compete in girls and women’s divisions. The issue, which on Thursday drew a handful of demonstrators to Georgia Tech’s campus, the site of the championships, had long buffeted the college sports industry. But it intensified as Thomas posted times that left opponents far behind and put some collegiate records under new pressure.

In December, Thomas recorded a 500 free time of 4:34.06, behind Katie Ledecky’s 4:24.06 mark from 2017. Thomas’s best time this season in the 200 free, 1:41.93, also posted in December, trailed the N.C.A.A. record of 1:39.10 that Missy Franklin set in 2015. Both Ledecky and Franklin are Olympic gold medalists.

The 200 free will be contested on Friday.

Thomas has said little in public this season, her final collegiate campaign to cap a distinguished career that included runner-up finishes in several men’s freestyle races at the Ivy League championships in 2019, even as her story rocketed from the insular swimming community onto talk shows and social media.

In an interview that Sports Illustrated published this month, not long after Thomas won this year’s Ivy League women’s championships in the 100-, 200- and 500-yard freestyle events, she said: “I don’t look into the negativity and the hate. I am here to swim.”

Her critics argued that was precisely the problem.

Through Nancy Hogshead-Makar, a lawyer who won three Olympic gold medals in swimming in the 1980s, more than a dozen members of Penn’s team sent an anonymous letter to the university and the Ivy League last month to complain that Thomas had “an unfair advantage over competition in the women’s category.” They cited her rapid ascension in the rankings, from high-quality conference swimmer to national title contender, and asserted that her potentially record-breaking times were “feats she could never have done as a male athlete.”

By then, though, the Ivy League had said it welcomed Thomas, who in 2019 came out to her team and began hormone replacement therapy, as a competitor in women’s swimming. (The Ivy League did not hold a 2020-21 season because of the coronavirus pandemic.)

The N.C.A.A., which five years ago played a role in nudging North Carolina away from a law that limited public restroom access for transgender people, saw its longstanding deliberations on transgender participation take on new urgency and intensity as Thomas swam in the women’s division.

But for all of the association’s efforts to depict a united front on the subject — John J. DeGioia, Georgetown University’s president and the chairman of the N.C.A.A.’s Board of Governors, said in January that officials were “steadfast in our support of transgender student-athletes and the fostering of fairness across college sports” — college sports leaders have been privately fractured over how, exactly, to proceed.

During a January meeting, the board divided over the timeline for the association’s updated policy on transgender participation, which it had unanimously approved and which called for the N.C.A.A. to follow “the policies of the sport’s national governing body.” Although the board normally works in lock step and rarely sees even one dissenting vote, the tally that afternoon was 12 to 7.

U.S.A. Swimming, the sport’s national governing body, soon tightened its rules in ways that Thomas’s supporters believed amounted to a poorly disguised effort to exclude her from the national championships. The N.C.A.A., though, ultimately decided not to let those more stringent protocols take effect this season, reasoning that “implementing additional changes at this time could have unfair and potentially detrimental impacts” on championship participants.

The N.C.A.A. would not make President Mark Emmert available for an interview. Many board members declined to be interviewed, referred inquiries to the N.C.A.A. or did not respond to requests for comment.

The association drew attention last year, when gay and transgender rights advocacy groups complained that a draft for a rewritten N.C.A.A. constitution did not include adequate protections against discrimination. And the association has waffled over its approach to holding major events, which can drive millions of dollars in spending, in states with laws seen as targeting transgender people.

Thomas and her rise, though, forced the typically plodding N.C.A.A. to grapple more quickly with a subject that scientists are still examining. Comprehensive research in athletes is still lacking, but early studies suggest that suppressing testosterone in transgender women decreases muscle mass and hemoglobin levels, reducing how much oxygen can be carried through the bloodstream.

Most of the changes occur within the first year of hormone suppression, but transgender women may still have more muscle mass than their cisgender peers even after three years. As some insist that no amount of testosterone suppression can undo the physiological changes linked to male puberty, like taller height and larger hands and feet, others dispute that transgender women have a built-in advantage and have argued that inclusion should outweigh competition.

The scientific and political debates, though, mattered only so much once Thomas plunged into the water at the McAuley Aquatic Center, just a few miles from the gold-topped State Capitol where Georgia lawmakers have spent part of the year clashing over a pending proposal to ban transgender students from interscholastic sports.

Azeen Ghorayshi contributed reporting.