The National Collegiate Athletic Association denied a spot in the final for Hungary's Reka Gyorgy by allowing Lia Thomas to compete.
There was a place in the consolation final for Gyorgy.
"It hurts me," Gyorgy reportedly said in a letter sent to the NCAA.
This is my last college meet and I am frustrated.
The final spot was taken away from me because of the NCAA decision to allow someone who is not a female to compete.
Hungary's Gyorgy competed in the Olympics for Hungary in 2016 and has been a member of the Virginia Tech swimming team for five years.
One place away from the B final, she finished 17th in the preliminary races for the 500-yard freestyle.
She would like to critique the NCAA rules that allow her to compete against us, but she acknowledged that Thomas is doing what she is passionate about and deserves that right.
I am writing this letter right now in hopes that the NCAA will change the rules in the future.
It doesn't promote our sport in a good way and I think it is disrespectful against the biologically female swimmers who are competing in the NCAA.
Thomas was on the Pennsylvania men's team for three seasons before starting hormone replacement therapy.
She broke records for her university swimming team.
The USA Swimming policy for elite swimmers was updated in February to allow trans athletes to swim in elite events, as well as reduce any unfair advantage, including testosterone tests for 36 months before the competition.
It said it will continue to champion gender equity and the inclusion of all cisgender and trans women and their rights to participate in sport, while also supporting competitive equity at elite levels of competition.
The new policy for elite athletes acknowledges a competitive difference in the male and female categories and the disadvantages this presents in elite head-to-head competition.
The NCAA decided that it would be wrong to implement the new rules mid-season, thus allowing Thomas to complete her final season.
Thomas won her 500m freestyle title in the NCAA Championships last week, but there were some protesters outside the venue and in the stands at Georgia Tech.
Thomas finished eighth in the 100 freestyle on Saturday, more than two seconds behind the winner, and tied for fifth in the 200 freestyle on Friday.
Iszac Henig, who identifies as a trans man but has not undergone any hormones, was competing in the 100m race.
The message "let trans kids play" was written on both Henig and Thomas' arms.
Henig said: "It was incredible. It was a dream come true. This entire meet is filled with incredible athletes - I just feel honoured to be here competing.
Henig said that it was important to him to do it and that he was glad that Lia was with him.
There are so many bills in so many different states that want to bar trans athletes, I think I need to use the platform I have to speak out, and that is really powerful for me.
Writing in Newsweek, US Olympic silver medallist Erica Sullivan - who competed against Thomas at last week's NCAA championships, said she was "proud to support" Thomas and backed her inclusion.
Lia has followed all of the rules and guidelines put before her and has trained diligently to get to where she is. Lia doesn't win every time. She deserves to be celebrated for her hard-won success, not labelled a cheat simply because of her identity.
As a woman in sports, I can tell you that there are real threats to women's sports, such as sexual abuse and harassment, and a lack of women in leadership.
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