The alleged victim, identified in court papers as Jane Doe, said she became a target of angry protests after Wesleyan officials recommended action against the Mu Epsilon chapter of Beta Theta Pi, the Hartford Courant reported.
The lawsuit, filed Friday in federal court, charges the university violated federal laws protecting women from discrimination.
"Wesleyan did nothing to prevent, and was deliberately indifferent to the harm caused to Jane Doe by the rape and outrageous sexual harassment and intimidation that followed her everywhere on campus," Doe's lawyers say in court papers.
Doe says the fraternity had a troubled past, but female students were not warned about it.
After the fraternity was barred from providing housing for its student members, Doe's identity became known on campus, the lawsuit said. Protesters picketed outside her dorm.
John O'Neill of Yorktown, N.Y., a guest of a fraternity member, pleaded no contest to lesser charges after he was charged with sexually assaulting Doe during a Halloween party in 2010. He was sentenced to 15 months.
Doe, a Maryland resident, later transferred to another school.