Background: In Colombia, the prevalence of overweight/obesity in children has increased by 26% in the past 5 years. School food environment may be an important contributor and offers opportunities for effective intervention. Methods: We conducted a cross-sectional study among 7- to 14-year-old schoolchildren from 10 schools in Bogotá, Colombia. We examined the school food environment and the relationship of individual-level consumption, and physical activity with overweight/obesity, measured by body mass index and percentage body fat. Results: Schools with a restaurant/store were characterized as having excessive unhealthy foods. In the sample of 714 schoolchildren, 17.5% were overweight and 10.5% were obese. In multivariate models, boys had significantly increased odds of being overweight/obese (odds ratio [OR]: 1.53; p = 0.01) as compared to girls. Schoolchildren who consumed a greater number of energy drinks (OR = 1.82; p = 0.04), and those who spent more than 3 hours per schoolday watching TV (OR = 1.53; p < 0.01) had increased odds of being overweight/obese. Conclusions: Approximately 1 in 4 schoolchildren were overweight/obese, with boys, energy drink consumers, and those with low physical activity having increased risk. School-based interventions focused on improving food options and providing health behavior education may be effective to reduce overweight among children in Bogotá and similar settings.