Starr announced his resignation on Wednesday and said in an interview his reason was due to "a matter of conscience."
An Outside the Lines report included a student of Baylor who claimed she was raped by a former Baylor football player who is now serving 20 years in prison. The student said she emailed Starr about her claims but received a response almost one week later from "someone in the university's Title IX office." There was no follow-up after the initial email exchange.
Starr claimed he was unaware of the sexual assault allegations against Baylor's football team until 2015, when media reports first appeared.
"I didn't know about what was happening, but I have to, and I willingly do accept responsibility. The captain goes down with the ship," Starr said.
Starr first became famous in the '90s when he acted as the special prosecutor in Clinton's notorious sex scandal with Lewinsky.
"We need to heal Baylor...We need to put this horrible situation behind us," Starr said.
Though he is no longer the school's president, Starr will remain at the university, teaching at the law school, according to reports.