Violence against women is a hot topic in the spotlight of contemporary science. In the academy, most of the courses are structured in a hierarchical system, in which students—especially female—become potentially vulnerable to emotional, physical and even sexual harm. This study aimed to describe the prevalence and the study-associated factors of emotional, physical and sexual violence against female students in medical, dental and psychological courses in South Brazil. A questionnaire-based survey was performed combining two previously validated tools for the investigation of workplace violence. The questionnaires were digitally provided to women undergoing medicine, dentistry and psychology courses in South Brazil. The study was conducted between April and July, 2018. The final sample consisted of 241 students (57 medical students; 91 dental students and 93 psychology students). Reports of general violence reached a prevalence rate of 45.2%. In particular, emotional violence reached 78.9% of the cases, whilst physical and sexual violence reached 4.6% and 8.3%, respectively. Amongst the identified offenders, professors figured as the most prevalent (18.4%). Alarming rates of violence against women were detected in this study. Institutional preventive strategies must be designed to protect female students in their study/workplace and enable a safe routine of academic activities.