Most studies on the prevalence of back pain have evaluated it in developed countries (Human Development Index--HDI > 0.808), and their conclusions may not hold for developing countries. The aim of this study was to identify the prevalence of back pain in representative Brazilian athletes from public high schools. This cross-sectional study was performed during the state phase of the 2015 Jogos dos Institutos Federais (JIF), or Federal Institutes Games, in Brazil (HDI = 0.744), and it enrolled 251 athletes, 173 males and 78 females (14-20 years old). The dependent variable was back pain, and the independent variables were demographic, socioeconomic, psychosocial, hereditary, exercise-level, anthropometric, strength, behavioral, and postural factors. The prevalence ratio (PR) was calculated using multivariable analysis according to the Poisson regression model (α = 0.05). The prevalence of back pain in the three months prior to the study was 43.7% (n = 104), and 26% of the athletes reported feeling back pain only once. Multivariable analysis showed that back pain was associated with demographic (sex), psychosocial (loneliness and loss of sleep in the previous year), hereditary (ethnicity, parental back pain), strength (lumbar and hand forces), anthropometric (body mass index), behavioral (sleeping time per night, reading and studying in bed, smoking habits in the previous month), and postural (sitting posture while writing, while on a bench, and while using a computer) variables. Participants who recorded higher levels of lumbar and manual forces reported a lower prevalence of back pain (PR < 0.79), whereas feeling lonely in the previous year, obesity, and ethnicity exhibited the highest prevalence ratio (PR > 1.30). In conclusion, there is no association between exercise levels and back pain but there is an association between back pain and non-exercise related variables.