Background: There is growing awareness of the need for effective prevention, early detection, and novel treatment approaches for common mental disorders (CMDs) among university students. Reliable epidemiological data on prevalence and correlates are the cornerstones of planning and implementing effective health services and adopting a public health approach to student wellness. Yet, there is a comparative lack of sound psychiatric epidemiological studies on CMDs among university students in low-and middle-income countries, like South Africa (SA). It is also unclear if historically marginalised groups of students are at increased risk for mental health problems in post-apartheid SA. The objective of the study was to investigate the prevalence and sociodemographic correlates of lifetime and 12-month CMDs among university students in SA, with a particular focus on vulnerability among students in historically excluded and marginalised segments of the population. Methods: Data were collected via self-report measures in an online survey of first-year students registered at two large universities (n = 1402). CMDs were assessed with previously-validated screening scales. Data were weighted and analysed using multivariate statistical methods. Results: A total of 38.5% of respondents reported at least one lifetime CMD, the most common being major depressive disorder (24.7%). Twelve-month prevalence of any CMD was 31.5%, with generalised anxiety disorder being the most common (20.8%). The median age of onset for any disorder was 15 years. The median proportional annual persistence of any disorder was 80.0%. Female students, students who reported an atypical sexual orientation, and students with disabilities were at significantly higher risk of any lifetime or 12-month disorder. Female gender, atypical sexual orientation, and disability were associated with elevated risk of internalising disorders, whereas male gender, identifying as White, and reporting an atypical sexual orientation were associated with elevated risk of externalising disorders. Older age, atypical sexual orientation, and disability were associated with elevated risk of bipolar spectrum disorder.