Sexual minority (SM) students are vulnerable to increased rates of psychological distress and harassment as a result of stigma and other forms of marginalization in the college environment. However, little research has been conducted on the experiences and psychological functioning among SMs who attend nonaffirming religiously affiliated universities (NARAUs) that enforce restrictive admission and conduct policies toward SM students, and/or view same-sex romantic expressions and identities as sinful. SM students (N = 213) attending NARAUs completed the Counseling Center Assessment of Psychological Symptoms (CCAPS), the Outness Inventory (OI), and the Lesbian, Gay and Bisexual Identity Scale (LGBIS). Results indicate that SM students who attend Mormon, Evangelical, and Nondenominational Christian NARAUs had more difficultly coming to terms with their sexual orientation than those in Catholic or Mainline Protestant schools. Furthermore, Mormon students reported significantly more incongruence between their sexual orientation and religious beliefs than other religious groups. Students who were involved with a Gay–Straight Alliance (GSA) had significantly less difficultly with their sexual orientation, less negative identities, and less religious incongruence than those students not involved with a GSA. More than 1 third (37%) reported being bullied or harassed at school because of their sexual orientation. Almost 1 in 5 (17%) reported a mental health professional had attempted to change their sexual orientation. Implications and recommendations for NARAU campus communities and counseling centers are discussed.