Objective Sport and scholastic factors are known to be associated with cigarette smoking in adolescence, but little is known about the causality of this association. The aim of this study was to prospectively explore the relationships of different sport and scholastic factors with smoking prevalence initiation in older adolescents from Bosnia and Herzegovina. Methods In this 2-year prospective cohort study, there were 872 adolescent participants (16 years at baseline; 46% females). The study consisted of baseline tests at the beginning of the third year (September 2013) and follow-up at the end of the fourth year of high school (late May to early June 2015). The independent variables were scholastic and sport-related factors. The dependent variables were (1) smoking at baseline, (2) smoking at follow-up and (3) smoking initiation over the course of the study. Logistic regressions controlling for age, gender and socioeconomic status were applied to define the relationships between independent and dependent variables. Results School absence at the baseline study was a significant predictor of smoking initiation during the course of the study (OR 1.4, 95% CI 1.1 to 1.8). Those who reported quitting sports at baseline showed an increased risk of smoking at the end of the study (OR 1.4, 95% CI 1.1 to 2.0) and of smoking initiation (OR 1.8, 95% CI 1.3 to 2.0). Adolescents who reported lower competitive achievements in sport were at a higher risk of (1) smoking at baseline (OR 1.5, 95% CI 1.1 to 2.1), (2) smoking at follow-up (OR 1.5, 95% CI 1.1 to 2.1) and (3) smoking initiation (OR 1.6, 95% CI 1.1 to 2.6). Conclusions In developing accurate antismoking public health policies for older adolescents, the most vulnerable groups should be targeted. The results showed that most participants initiated smoking before 16 years of age. Therefore, further investigations should evaluate the predictors of smoking in younger ages.