PURPOSE: This study aimed to examine both independent and dependent longitudinal associations of physical fitness (PF) components with academic achievement. METHODS: A total of 954 fourth to seventh graders (9-15 yr [Mage = 12.5 yr], 52% girls) from nine schools throughout Finland participated in a 2-yr follow-up study. Register-based academic achievement scores (grade point average [GPA]) and PF were assessed in the spring of 2013-2015. Aerobic fitness was measured with a maximal 20-m shuttle run test, muscular fitness with curl-up and push-up tests, and motor skills with a 5-leaps test and a throwing-catching combination test. Structural equation modeling was applied to examine the longitudinal associations adjusting for age, gender, pubertal stage, body fat percentage, learning difficulties, and mother's education. RESULTS: The changes in aerobic and muscular fitness were positively associated with the changes in GPA (B = 0.27, 99% confidence interval [CI] = 0.06-0.48; B = 0.36, 99% CI = 0.11-0.63, respectively), whereas the changes in motor skills were not associated with the changes in GPA. Better motor skills in year 2 predicted better GPA a year later (B = 0.06, 99% CI = 0.00-0.11; B = 0.06, 99% CI = 0.01-0.11), whereas aerobic and muscular fitness did not predict GPA. GPA in year 1 predicted both aerobic (B = 0.08, 99% CI = 0.01-0.15) and muscular (B = 0.08, 99% CI = 0.02-0.15) fitness, and motor skills (B = 0.08, 99% CI = 0.02-0.15) a year later. CONCLUSION: The changes in both aerobic and muscular fitness were positively associated with the changes in academic achievement during adolescence, whereas the changes in motor skills had only borderline significant association. However, better motor skills, although not systematically, independently predicted better academic achievement 1 yr later, whereas aerobic or muscular fitness did not. Better academic achievement predicted better motor skills, aerobic fitness, and muscular fitness. Developmental changes in adolescence may induce parallel and simultaneous changes in academic achievement and PF.