Physical exercise results in an active well-being. It is likely that students' engagement in physical exercise keeps them motivated to perform academic endeavors. This study aimed to assess the relation of time engaged in physical exercise with medical students' motivation for academic work. Prospectively, 296 second-year medical students self-administered Vallerand's Academic Motivation Scale. The frequency of exercise per week and the duration per time were multiplied to compute a weekly physical exercise engagement time. Multivariable regression model treated the intrinsic motivation construct as the dependent variable, adjusting relevant covariates such as sleeping time, sitting time, screen time, and vegetable intake. The level of intrinsic motivation was positively related to the student's physical exercise time per week (ß 0.85, 95% confidence interval 0.42-1.26, p-value < 0.001). Thus, generating conditions in which students can engage in physical exercise may contribute to fostering their intrinsic motivation for academic work.