INTRODUCTION: Knowledge about student motivation allows educators to broaden their understanding and to establish strategies that make it possible to enhance motivation. OBJECTIVES: To investigate the levels of student motivation at different phases of medical education, comparing incoming students' motivation with that of those at the end of their studies, as well as during the different preclinical, clinical, and clerkship cycles. METHOD: Cross-sectional study including students from a Brazilian public university. The questionnaire included sociodemographic data and the Academic Motivation Scale (AMS). Student motivation was compared at different phases of the medical course. RESULTS: 710 students were included. Students in the preclinical phase (1st-2nd years) had higher levels of integrated regulation AMS (e.g.,"Education is a privilege."), introjected regulation AMS (e.g."I come because it is what is expected of me."), and intrinsic motivation AMS (e.g."School is a pleasure"). Students in the clinical phase (3rd-4th years) had higher levels of amotivation (e.g., "I'm wasting my time at school.") and external regulation AMS (e.g., "I'm coming to school to earn a degree"). AMS levels of external regulation, introjected relation, and integrated regulation were different for Clerkship students (5th-6th years) compared to preclinical students, but not for clinical students. Comparing only the first and last years, incoming students had higher levels of integrated regulation AMS and lower levels of amotivation AMS and external regulation AMS. CONCLUSION: Important motivational changes were found during different phases of medical school, with higher levels of motivation during the course's initial semesters. These findings can aid in developing educational strategies to stimulate self-determined education.