The latest data on physical inactivity among young university students raise concerns about the quality of life and development of this population. The scientific literature indicates that the motivation to practice physical activity is largely influenced by the sex of the students. The aim of this study is to analyze the existing differences in the motivation to practice physical activity in university students from Extremadura according to their sex. For this purpose, the Physical Activity Motivation Measurement Scale (MPAM-R) was applied. In order to explore the possible differences between both sexes, the Mann-Whitney U test was used, together with the Hedges' g to assess the effect size. Likewise, the possible associations between the dimensions of the questionnaire, age and physical activity levels of the students were explored. The results showed significant differences in the motivations for physical activity between men and women, in the items of enjoyment, appearance, social, fitness and competence, therefore, the practice of physical activity in the university population seems to be an effective strategy to improve physical and mental health, acquiring vital importance as a protective factor against numerous psychological and social disorders. Interventions that promote the practice of physical activity by focusing on the main motivations of the student body can create greater adherence to this practice and, therefore, improve healthy habits among university students.