Objective: Research suggests that women experience more barriers to physical exercise than men do. Advocating for increased physical exercise is a primary responsibility of professionals who have specialised in the field of physical activity and sports sciences. This study aimed to examine differences in barriers to the practise of physical exercise, and the general state of mental health, among university students of physical activity and sports sciences based on gender. Design: A cross-sectional analysis of 144 students attending physical activity and sports sciences courses. Setting: Participants were recruited from a university in Spain. Method: This study used the validated Spanish versions of the Self-Report of Barriers to the Practice of Physical Exercise questionnaire and the 12-item General Health Questionnaire. Results: Based on the total Self Report of Barriers to the Practice of Physical Exercise questionnaire and total 12-item General Health Questionnaire scores, female students reported significantly higher barriers and significantly poorer mental health than male students did. A weak positive correlation was observed between the total Self-Report of Barriers to the Practice of Physical Exercise questionnaire and 12-item General Health Questionnaire scores. Conclusion: Among university students who studied physical activity and sports sciences, women perceive greater barriers to physical exercise than men did, even though both groups had an inherent interest in exercise. A perception of greater barriers to engaging in physical exercise was associated with a negative impact on overall mental health, suggesting the need to address these barriers in future research on students of physical activity and sports sciences.