The purpose of this study was to explore individual, interpersonal, and organizational factors that may influence the physical activity of adolescents (ages 10–14) in Pakistani schools. A set of questionnaires that included individual, interpersonal, and organizational factors and PA behavior was completed by the 618 students selected from Pakistani schools. Stepwise forward regression model was applied to check the possible effects of multilevel variables on physical activity and to extract the stronger predictors. The results showed that physical activity was significantly predicted by individual level factors such as self-efficacy, motivation, and attitude. Among the demographic correlates, gender, age, and BMI did not affect physical activity, while socioeconomic status and geographic characteristics had a meaningful association with PA. At the interpersonal level, adolescents’ perception of family support had a potential influence on physical activity, while there was no impact of friends/peers and teachers support on adolescents’ PA. A school environmental characteristic, such as PA facility, was positively related to PA; however, the impact of PA equipment, safety, and policy and PA culture were statistically non-significant. The findings suggest that public health intervention strategies aimed at promoting PA in adolescents should recognize multiple levels of influences that may either enhance or impede the likelihood of PA among adolescents.