Background: Medical students from ethnic minorities underperform in knowledge and skills assessments both in pre-clinical and clinical education compared to the ethnic majority group. Motivation, which influences learning and academic performance of medical students, might play an important role in explaining these differences, but is under-investigated. This study aimed to compare two types of motivation (autonomous and controlled) of ethnic minority (Western and non-Western) and majority (Dutch) students, and their association with academic performance. Methods: In a cross-sectional study, all students of a Dutch medical school were invited to complete a survey including the Academic Self-Regulation Questionnaire, measuring autonomous and controlled motivation, in the academic year 2015-2016. Motivation was compared using Kruskal-Wallis test and performance was compared using One-Way ANOVA. Linear regression analysis was used to determine the association between motivation and performance (grade point average; GPA). Results: The response rate was 38.6% (n = 947). Autonomous motivation (AM) of non-Western students was higher than that of Dutch students in pre-clinical and clinical education (p < 0.05). Controlled motivation was higher in Western students than in Dutch students (pre-clinical education; p < 0.05). AM was associated with a higher GPA for Dutch (pre-clinical education; β = 0.33, p < 0.05) and Western students (clinical education; β = 0.57, p < 0.05) only. Conclusions: Our results show significant differences in the type of motivation between the ethnic majority and minority groups. The association of motivation with performance also differs between ethnic groups. We found that AM has a positive influence on GPA. Further research is needed to uncover the underlying mechanisms.