The apology comes amid an investigation by the Trump Department of Education over Title IX violations.
The school will also bar males from female sports teams moving ahead.
Though a late gesture after a forced hand, the apology struck a chord of emotion for many.
"I was in the room yesterday at the White House when Secretary Linda McMahon made the announcement that UPenn was going to revise the records and remove William Thomas from those records but also issue an apology, a written apology on UPenn letterhead to all the girls are impacted by this. It was very emotional. I've got three daughters that I care very much about, but the big thing is that we're all being vindicated,” Terry Schilling, of American Principles Project, told AFN.
Will Thomas claims he is a female and wants to go by the name Lia. Still, female athletes, including former University of Pennsylvania swimmer Paula Scanlan (shown at right), called it unfair and a violation of Title IX.
"More than anything, I'm grateful for this administration for taking it so seriously," Scanlan, speaking at the White House, said Tuesday. "I have gotten exactly what I voted for."
Scanlan went on to described how the university forced her and her female teammates to have to undress in the same locker room as the 6-foot-4 Thomas.
"In addition, he broke every record in every event he swam, went on to win an NCAA championship title and also every single time Thomas competed on behalf of the U of Penn, a girl on the team was asked to stay home," said Scanlan.
A second UPenn swimmer, Margo Kaczorowski, told Fox News stripping Thomas of his achievements is a good "starting point" to protect female athletes, but she added there is "long way to go" on the issue.
She thanked the Trump administration for taking the side that protects women, but she pointed out UPenn is only backtracking and apologizing under pressure from the federal government.
'Wrong side of history' hasn't aged well
When she and others tried to speak out about Thomas, Scanlan said the university sat them down and told them to avoid criticism or "be on the wrong side of history" with this issue.
"They said you will be tainted by this, that you'll never be able to find a job," said Scanlan. "They told us that if we didn't want this man in the locker room, it was equivalent to not wanting to undress to someone based on their race in the 1960s."
For Schilling, there’s a great sense of relief.
"We were talking about this idea that men were competing against women in sports simply by claiming to be women, and what an injustice it was, and we were gas lit for so long. Yesterday was the vindication that so many that were involved in this fight were looking for: an apology, the fixing and repairing of the records and getting back to basics by kicking men who identify as women out of women's sports. It was a beautiful day."
