Background: To examine associations of cardiorespiratory fitness, physical activity (PA) and weight status with academic achievement 1 year later. In addition, the mediating role of psychological variables was tested. Methods: Longitudinal analyses included 1011 German students (M = 14.1 years, SD = 0.6 years). Cardiorespiratory fitness was determined with the 20 m shuttle run test. Compliance with PA guidelines was assessed through questionnaire. Weight status was based on body mass index percentiles. As proxy of academic achievement students' self-reported grades in Mathematics and German in their midterm report were averaged. Mediation analyses were conducted at follow-up testing general self-efficacy, depressed affect, and attention/hyperactivity problems. Results: High levels of cardiorespiratory fitness predicted higher educational attainment (p = 0.007), while we found no longitudinal association for PA and weight status (p > 0.253). However, students being insufficiently physically active at baseline but meet PA guidelines at follow-up showed a significant improvement in educational attainment. The cross-sectional association between PA and academic achievement was mediated by students' general self-efficacy. Conclusion: High fitness in adolescence is associated with higher subsequent academic achievement. The promotion of PA might benefit school performance because of enhanced fitness levels in the long-term and positive influences of PA in the short-term. The association between weight status and educational attainment remains controversial.