Former head coach Art Briles is also being cited along with the university.
The NCAA served Baylor with a "formal notice of allegations" regarding the university's handling of sexual assault allegations on Monday, according to the Fort Worth Star-Telegram.
Baylor is being cited for a "lack of institutional control," while former head coach Art Briles has been cited for "failing to promote an atmosphere of compliance."
The NCAA reportedly opened its investigation into Baylor in 2017, and finished its report in September. The case is likely to be resolved in "the spring of 2019" per the Star-Telegram.
Baylor has dealt with a slate of sexual assault incidents both during and after Briles's tenure, including failure to respond to reports of rape and/or sexual assault filed by at least six female students from 2009 to 2016. Briles was fired in May 2016, while former Baylor athletic director Ian McCaw and president Ken Starr resigned.