Objective To evaluate the association between migration and physical activity among medical students from a university located in Lima, Peru. Methods A cross-sectional study was conducted among second-year medical students from a Peruvian university. Data on moderate- to vigorous-intensity physical activity (MVPA) and migration features were obtained through a self-report questionnaire. To assess the associations of interest, prevalence ratios (PR) along with their 95% confidence intervals (95% CI) were calculated using Poisson regression with robust variances. Results We analyzed data from 312 students (54.5% were women, mean age: 19.0 years, standard deviation: 1.4 years), 90 (28.9%) students performed MVPA for 150 minutes/week, 118 (37.8%) performed MVPA for 30 minutes/week, and 114 (36.7%) were migrants. Being a migrant was not associated with performing MVPA for 30 nor 150 minutes/week. However, adjusted analysis showed that the frequency of performing MVPA for 30 minutes/ week was greater among those who migrated less than five years ago (PR: 1.43; 95% CI: 1.05–1.93) and among those who migrated to continue their studies (PR: 1.44; 95% CI: 1.06–1.94), compared to non-migrants. Conclusion In our population, being a migrant was not associated with physical activity. However, low physical activity was more prevalent among recent migrants and among those who had migrated to study, compared to non-migrants.