To identify the predictors of dropout in the 'Mexa-se' intervention according to the body mass index (BMI) category. This was a controlled, non-randomized study. The intervention included: (i) increase in the intensity of physical activities (PA) in physical education (PE) classes; (ii) active recess; (iii) educational sessions on PA, nutrition and body image; and (iv) educational materials. Dropout was considered when students dropped out of intervention, or did not reach 75% attendance in PE classes. The independent variables were gender, age, study period, socioeconomic status, BMI, PA, screen time, food consumption, health perception, attitudes toward PA, self-efficacy for PA, perception of the school environment, body image and self-esteem. Binary logistic regression analysis was used. The dropout rate was 26.8%. In the total sample and among students with an adequate BMI, there was a greater probability of dropout with an increase in age. For overweight students, increased age and socioeconomic status, and studying in the afternoon period were predictors of dropout from the intervention. Socio-demographic factors were predictors of dropout from the 'Mexa-se' intervention; the associated factors differed based on the BMI category.