PHILADELPHIA — The University of Pennsylvania will send “personalized” letters of apology to its female athletes who felt aggrieved by transgender swimmer Lia Thomas’ participation on their team and restore Penn records and honors they would have won if not for Thomas, as part of a resolution agreement reached with the federal government.

At least in this case, Penn becomes the first Ivy League university to strike a truce with President Donald Trump’s administration since it began targeting some of the nation’s elite universities, threatening funding and damaging policy changes if they don’t comply with certain demands.

It was not immediately clear whether the deal would result in the restoration of $175 million in federal funding to Penn that the White House said was paused in March, citing Thomas’ participation.

According to a two-page document obtained by The Inquirer, Penn has also agreed to issue a public statement, which will be posted prominently on its website, saying that it will abide by Title IX — the civil rights law that prohibits sexual harassment and discrimination — “as interpreted by the Department of Education.” But the agreement is restricted only to athletics and doesn’t affect other areas of university operations.

Perhaps most controversially, the school said it would specifically cite by name Trump’s executive order titled “Defending Women From Gender Ideology Extremism and Restoring Biological Truth to the Federal Government” and state that all its “practices, policies, and procedures adopted and implemented by the university with respect to women’s athletics” will comply with that order, as well as a similar order issued in February.

The university’s women’s athletic policies will adhere to the words “sex,” “female,” “male,” “women,” and “men” as defined in Trump’s executive order, the resolution states.

“We have now brought to a close an investigation that, if unresolved, could have had significant and lasting implications for the University of Pennsylvania,” President J. Larry Jameson said in a statement to the Penn community.

“Our commitment to ensuring a respectful and welcoming environment for all of our students is unwavering. At the same time, we must comply with federal requirements, including executive orders, and NCAA eligibility rules, so our teams and student athletes may engage in competitive intercollegiate sports.”

Penn in February scrubbed diversity initiatives from its websites and programming to comply with another Trump order that threatened funding to colleges that employ diversity efforts.

The Department of Education did not immediately respond to a request for comment.

The Trump administration in late April said Penn had violated federal civil rights law by allowing Thomas to compete during the 2021-22 season and use the female facilities. The department demanded that the university apologize to affected female swimmers and restore accolades they would have won. It also issued other demands and gave Penn 10 days to respond — a deadline that passed nearly two months ago. The department said failure to comply would put the Ivy League university’s funding at risk.

Neither the university nor the department had responded to repeated questions on what was happening after the deadline passed until the resolution was reached.

The agreement does not address that $175 million in paused funding.

Thomas’ participation on Penn’s team drew national attention and stirred debate over trans athletes’ right to play sports. Thomas became an Ivy League champion and broke records at the women’s swimming and diving championships held at Harvard in February 2022.

When Thomas competed, the NCAA allowed transgender athletes; the association modified its rules earlier this year and banned transgender athletes from women’s sports in response to the executive order by Trump.

Thomas was the first and only transgender woman athlete to have competed at Penn, and since then, there have been no others.

Under the agreement, Penn acknowledged that even if the NCAA were to change its policies again, Title IX would “supersede” it, raising questions about what would happen to Penn athletes if the association decided to allow trans athletes to compete in women’s sports again. But it’s highly unlikely that the association would do that unless the education department, under a new presidential administration, altered its interpretation of Title IX back to the previous iteration.

Resolution agreements are not uncommon in civil rights cases brought by the department. In 2024, the department received more than 11,800 Title IX cases and resolved more than a third of them. Drexel University entered into one last August, vowing to improve its handling of antisemitism complaints. So did Temple University.

Exactly what the department wanted in the Thomas case was a little unclear, given that she no longer competes, that Penn has said no other transgender athletes have competed on female teams since that time, and that Penn has stated previously it no longer allows transgender athletes to compete on women’s sports because of the new NCAA guidelines.

Under the resolution agreement, Penn stated the same, that it “will not allow male students to compete in any athletic program restricted to women” and that it would provide separate locker rooms and bathrooms for the athletes based on sex.

The school promised to adjust statements and information on its websites to be in full compliance with the resolution agreement and provide evidence it has done so to the department. It will do the same for school records and titles previously held by Thomas and restored to other swimmers, whether they are current students or have since graduated.

In his campus communication, Jameson said even though Penn complied with NCAA rules when it allowed Thomas to compete, “we acknowledge that some student-athletes were disadvantaged by these rules. We recognize this and will apologize to those who experienced a competitive disadvantage or experienced anxiety because of the policies in effect at the time.”

One of the previous demands made by the department seems to have fallen away. It initially said Penn must change Ivy League and national championship records held by Thomas, something the university had said it doesn’t have the power to do. That was not addressed in the agreement.

Penn’s action comes as Trump threatens federal funding for universities in an attempt to reshape higher education to match his agenda. While its demands on Penn at least so far have been limited to transgender athlete participation, its demands on Harvard University and Columbia University have been much more far-reaching, seeking to limit student activism, end diversity programs and exert control over security, admissions, hiring and some academic programs,

Harvard had publicly refused to meet Trump’s demands and in return the White House said it would end the school’s federal funding and has threatened its tax exempt status and its international student enrollment. But Harvard officials now are considering a possible truce with the federal government, The New York Times reported last week.

Columbia University agreed to a series of demands, but the Trump administration later announced it would go after the school’s accreditation.

On Friday, James Ryan, the president of the University of Virginia, resigned under pressure from the Department of Justice that demanded he step down to resolve an investigation into whether the school had complied with Trump’s orders regarding diversity, equity and inclusion.

Penn is also facing another federal inquiry into its foreign funding; it’s not yet clear whether the administration will make more demands of Penn based on that investigation.

Jameson said Penn “remains committed to fostering a community that is welcoming, inclusive, and open to all students, faculty, and staff. I share this commitment, just as I remain dedicated to preserving and advancing the University’s vital and enduring mission.”

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