Abstract Background Students entering medical school are driven by different types of motivation: autonomous motivation, controlled motivation, or amotivation. Motivation types can influence students’ performance, outcome and well-being. To our knowledge, this topic has never been studied in Lebanese medical students. This study aims to identify students’ motivation types in the first 5 years of medical school at two Lebanese universities (USJ and USEK). It also aims to determine the predominant motivation type of the whole sample. Results may be the first step towards raising awareness about this topic and implementing actions that enhance autonomous motivation. Methods A cross-sectional study was performed between January and June 2017. A questionnaire was sent to medical students by e-mail. The students’ academic motivation was assessed using the Academic Motivation Scale. Results A higher mean autonomous motivation score was found in each academic year, as compared to the mean controlled motivation and amotivation scores. The highest mean autonomous motivation score was seen among second year students, whereas the lowest score was noted in fifth year students. The highest scores for controlled motivation and amotivation belonged to the fourth-year students, and the lowest to the first-year students. Students who were still satisfied with medical studies had a higher autonomous motivation score. Finally, USJ students who were satisfied with their second year training had a higher mean autonomous motivation score than those who were not. Conclusion This study showed high levels of autonomous motivation in the first five years of medical school. Autonomous motivation was the predominant type in the whole sample. The highest scores of controlled motivation and amotivation were noted in the fourth year. Moreover, high levels of self-determination were seen in students who enjoyed their early contacts with patients through trainings. Actions should be implemented in medical schools to enhance and maintain autonomous motivation, and consequently students’ outcome and health-care quality.