Now Thomas is being hailed as one of the best women's collegiate swimmers in the country, with her rapid success prompting both praise and criticism in the swimming world.
Transgender athletes will now have mandatory testosterone testing starting with the 2022-23 academic year -- at the beginning of their season and again six months later, according to rules approved this week by the NCAA Board of Governors. Additionally, they will need to test four weeks before championship selections.
The NCAA previously required that transgender women have testosterone suppression treatment for a year before competing on a women's team.
Penn Athletics said it will work with the NCAA regarding Thomas' participation in the 2022 swimming and diving championship in March.
Still, from the association representing college swimming and diving coaches to former Olympic swimmers to the parents of women swimmers at the collegiate level, the NCAA's new policy is being criticized as insufficient and lacking clarity.
CNN has sought comment from the NCAA about the criticism.
"They're doing this in the middle of the season and it's clear that they haven't entirely thought everything out," said Joanna Harper, a transgender runner who is researching transgender athletic performance at England's Loughborough University.
Harper, a medical physicist who published the first study of testosterone suppression and estrogen treatment on the performance of transgender athletes, added: "I don't think this policy, for instance, will affect Lia Thomas one bit, and people are going to be unhappy because she's doing well."
Thomas, 22, has not publicly commented on the new policy. She told SwimSwam Podcast
last month that "continuing to swim after transitioning has been an incredibly rewarding experience." She said she hoped to "continue to do the sport I love as my authentic self."
Policy in line with that of Olympic committees
The NCAA this week voted in favor a "sport-by-sport approach to transgender participation"
it said was consistent with the US and International Olympic Committees.
Transgender participation for each sport will be determined by the policy for the sport's national governing body. In the absence of a national governing body, the policy of a sport's international federation would apply. And if there is no international federation policy, "previously established IOC policy criteria would be followed," according to an association statement.
"We are steadfast in our support of transgender student-athletes and the fostering of fairness across college sports," said John DeGioia, chair of the NCAA board and Georgetown president.
"It is important that NCAA member schools, conferences and college athletes compete in an inclusive, fair, safe and respectful environment and can move forward with a clear understanding of the new policy."
About 80 percent of US Olympians are current or former college athletes, according to NCAA President Mark Emmert.
The IOC in November announced a new framework on transgender athletes,
saying no athlete should be excluded from competition on the assumption of an advantage due to their gender. The change placed the responsibility on individual sporting federations to determine if an athlete was at a disproportionate advantage.
The IOC's previous policy allowed transgender athletes to compete provided their testosterone levels were below a certain limit for at least 12 months before competition.
Thomas addressed the IOC framework in her interview with Swimswam: "I think the guidelines they set forward are very good. They do a very good job of promoting inclusivity while keeping competitional integrity going."
Penn Athletics says it supports Thomas
At the University of Pennsylvania, parents of other swimmers have questioned the fairness of allowing Thomas to race on the women's team.
The mother of a female swimmer at Penn said her concern is about fairness and the 1972 Title IX provision banning discrimination on the basis of sex at schools receiving federal funding that in her words "allowed women to shine in athletics."
Title IX is credited an explosion of women in collegiate athletics and schools pouring money into female sports.
"Girls who dedicate their lives to swimming, they start really early," said the mother, who asked not to be identified for fear of reprisals against her daughter. "They never miss practices. They wake up at 5 a.m. starting from age 12. They don't take vacations."
This mother and another parent worry that Thomas' success could come at the expense of their own daughters' chances to travel and compete because of roster limits.
"My daughter, for instance, all through high school, she trained upwards of 20 hours a week," said the other parent, a father who asked to remain anonymous.
"Her only day off was Sunday. In addition to maintaining the kind of academics required to get accepted to a school like the University of Pennsylvania. She worked for four years through high school for that. Not to mention all of the years prior to high school that led up to that. And then to be told that you and your teammates are going to lose spots to a transgender woman."
In a statement, Penn Athletics said it supports Thomas and "we will work with the NCAA regarding her participation under the newly adopted standards for the 2022 NCAA Swimming and Diving Championship."
Former Olympic swimmer Nancy Hogshead-Makar, who runs a nonprofit that offers legal advocacy for women in sports, said she agreed with the new policy since it would require transgender swimmers like Thomas to report their testosterone levels four weeks before the championship selections.
But she called the new policy unfair because of what she perceives as Thomas' biological advantage.
'Policy is a direct response to pressure'
The College Swimming & Diving Coaches Association
, in a statement, this week supported Thomas' right to compete and condemned the "hatred" directed at her. But the association also said the new NCAA policy is "not a solution" and a "missed opportunity to lead" in a "thorough, thoughtful, and scientific discussion about the balance of inclusion and fairness."
USA Swimming, the national governing body for the sport in the US, expressed support for "inclusivity" and "competitive equity." In the statement, the organization vowed "to learn and educate ourselves on the appropriate balance in this space."
Chris Mosier, a transgender athlete and advocate, via Twitter said the NCAA has "whipped up a ridiculously complex policy that will prove impossible for them to follow."
"It is clear this policy is a direct response to pressure surrounding a current athlete competing in the NCAA," Mosier said in a joint statement with Athlete Ally,
a group that supports LGBTQ athletes.
"It is disappointing to me that after years of discussions and calls for more research, a new policy could be quickly assembled under pressure from people who don't want to see a great athlete who is transgender succeed."
The controversy surrounding Thomas comes at a time when a number of state legislatures have banned transgender girls and women i
n public secondary schools and colleges from participating on girls and women's sports teams.
Controversy 'hugely overblown,' researcher says
Harper, who is transgender, estimated that about 50 of the roughly 200,000 athletes competing in women's sports at the collegiate level in the US are transgender.
In 2015, Harper published the first study on how hormone therapy affected transgender athletes. It found that transgender distance runners had no inherent advantage as women. The study involved a small sample of runners, she said, adding that the muscle mass of transgender sprinters could be advantageous for them in shorter races.
Eric Vilain, a geneticist who specializes in gender-based biology at George Washington University, called Harper's study "groundbreaking" in a 2018 article in Sciene
-- a peer-reviewed journal published by the American Association for the Advancement of Science.
Still, there is heated debate in the scientific community as to whether androgenic hormones like testosterone are useful markers of athletic advantage, according to experts.
Harper said the controversy over Thomas record-breaking season stems from her domination in the sport.
"I think a lot of the heat over Lia Thomas is just hugely overblown," Harper said.
"Trans women don't transition for sports. We transition to be more like other women. And so as part of this therapy to be happier, healthier ... trans women will undertake this therapy and will have testosterone levels in compliance because it's for their health, not because it's has anything to do with sports."