Objective: to identify the factors associated with overweight and obesity in students of high school of an Andean region of northern of Peru. Methods: a cross sectional study was performed in a sample of 586 students, residing in two districts of Cajamarca region. We performed the anthropometric evaluation using the standards of child growth of the World Health Organization (using the score z of the body mass index). We applied a structured survey for recollect data of lifestyles, food consumption, physical activity, depressive symptoms questionnaire, bullying and weight perception. A multivariate logistic regression analysis was performed to identify associated characteristics. Results: the percentage of overweight and obesity was 22.9% and 6.8% of adolescents, respectively. Attending public schools was a protective factor for overweight (adjusted OR: 0.62, CI 95%: 0.39 to 0.99) regardless of gender, physical activity and depressive symptoms. Male gender (adjusted OR 2.05, 95% CI: 1.02 to 4.11) and low physical activity (adjusted OR: 4.14, 95% CI: 1.65 to 10.35) were risk factors for obesity, while attending public schools was a protective factor (adjusted OR 0.43, 95% CI: 0.20 to 0.92). Conclusions: the level of physical activity is the main factor associated with obesity; on the other hand, public school students are less likely to be overweight and obesity. Schools represent good environments to implement interventions that prevent overweight and obesity based on increased physical activity.