© 2019 Zevallos-Morales et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. 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.