The objective was to determine the prevalence of lower back pain in adolescents and its relationship to sports and sedentary activities. We conducted a cross-sectional study of 5th to 8th-grade students (n = 1,236) in Bauru, São Paulo State, Brazil. We used a structured protocol and the Nordic questionnaire for musculoskeletal symptoms. The analysis was performed using a descriptive approach and bivariate and multivariate binary logistic regression. Prevalence of lower back pain was 19.5% (7% in boys and 12.5% in girls), with statistically significant differences according to gender (p < 0.00001), age (p = 0.0057), and sports (p = 0.0001). Bivariate and multivariate analyses showed independent associations between lower back pain and female gender, time watching TV, and sports. Lower back pain in schoolchildren can persist as chronic pain in adults. Understanding the relationships between variables should provide useful measures for maintaining, improving, and promoting students' wellbeing.