Thomas began swimming on the men's team at the University of Pennsylvania in 2017, and during her freshman year, recorded a time of 8 minutes and 57.55 seconds in the 1,000-yard freestyle that ranked as the sixth-fastest national men's time, as well as 500-yard freestyle and 1,650-yard freestyle times ranked within the national top 100.[4] On the men's swim team in 2018–2019, Thomas finished second in the men’s 500, 1,000, and 1,650-yard freestyle at the Ivy League championships as a sophomore in 2019.[4][3][7] During the 2018–2019 season, Thomas recorded the top university men's team times in the 500 free, 1000 free, and 1650 free.
Thomas lost muscle mass and strength through testosterone suppression and hormone replacement therapy. Her time for the 500 freestyle is over 15 seconds slower than her personal bests before medically transitioning.[12][13] Thomas's event progression peaked in 2019 for distance swimming, with a drop in times during the 2021–22 season. Her event progression for sprint swimming reflected a dip at the start of 2021–22 season before returning to near-lifetime bests in the 100 free and a lifetime personal best in the 50 free in 2021.[14]
In the 2018–2019 season she was, when competing in the men's team, ranked 554 in the 200 freestyle, 65 in the 500 freestyle, and 32 in the 1650 freestyle. In the 2021–2022 season, those ranks are now, when competing in the women's team, 5 in the 200 freestyle, first in the 500 freestyle, and eight in the 1650 freestyle.[15][16] According to an archived page of the swimming data website Swimcloud, Thomas was ranked 89th among male college swimmers for that season.[17]
In a race during January 2022 at a meet against UPenn's Ivy League rival Yale, Thomas finished in 6th place in the 100m freestyle race, losing to four cisgender women and Iszac Henig, a transgender man, who transitioned without hormone therapy.[18][19]
In March 2022, Thomas became the first openly transgender athlete to win an NCAA Division I national championship in any sport, after winning the women's 500-yard freestyle with a time of 4:33.24; Olympic silver medalist Emma Weyant was second with a time 1.75 seconds behind Thomas.[20][21][22] Thomas did not break any records at the NCAA event, while Kate Douglass broke 18 NCAA records.[23] Thomas was 9.18 seconds short of Katie Ledecky's NCAA record of 4:24.06.[24] In the preliminaries for the 200 freestyle, Thomas finished second. In the final for the 200 freestyle, Thomas placed fifth with a time of 1:43.50. In the preliminaries for the 100 freestyle, Thomas finished tenth. In the finals for the 100 freestyle, Thomas placed eighth out of eight competitors in 48.18 seconds, finishing last.[25]
The March 2022 NCAA championship was Thomas's last college swimming event.[26] By the conclusion of Thomas's swimming career at UPenn in 2022, her rank had moved from 65th on the men's team to 1st on the women's team in the 500-yard freestyle, and 554th on the men's team to 5th on the women's team in the 200-yard freestyle.[27][15] According to the swimming data website Swimcloud, Thomas is ranked 36th among female college swimmers in the United States for the 2021–2022 season,[28] and 46th among women swimmers nationally.[29] According to Sports Illustrated, she has applied for law school and plans to swim at the 2024 Summer Olympics trials.[2]