Positive association between physical fitness and academic achievement in adolescents has been suggested yet the causal effect of physical fitness on academic achievement remains unclear. This study examined if longitudinal changes in physical fitness were associated with changes in academic achievement among junior high school students. Analyses were based on a two-year with three time-point data of 567 students (aged 12⁻13 years old at the baseline-point; 303 boys) who entered in five Japanese junior high schools in 2015. Academic achievement was evaluated using the student's overall grade point average. Comprehensive physical fitness score was summed up from eight fitness tests: 50-m sprint, standing broad jump, repeated side-steps, sit and reach, sit-ups, hand-grip strength, handball throw, and 20-m shuttle run or endurance run. The hybrid regression model was applied to examine the impact of change in physical fitness on change in academic achievement using multiple imputation to account for non-response at follow-up. The changes in fitness score within-person and the differences in average of fitness score of three-time points between-person were associated with change in overall grade point average for boys. No significant association between fitness score and overall grade point average was observed in girls. Opportunities for increased physical fitness may be important to support academic achievement, particularly in junior high school boys.