The purpose of this study was to examine the potential role of aerobic fitness (AF) as a mediator of the association between physical activity (PA) and academic achievement (AA) among Japanese junior high school students. A cross-sectional data was collected from 608 7th grade students enrolled at five public junior high schools in two suburban municipalities in Okinawa, Japan. Self-reported PA was assessed using the Patient-Centred Assessment and Counselling for Exercise plus Nutrition questionnaire. The 20-meter shuttle run test was performed to determine AF. AA was evaluated using the overall grade point average. Family structure, parental education level, and achievement motives were the self-reported covariates. The results of the bootstrapped mediation analysis indicated that PA had a direct effect on AF, which in turn influenced the AA among boys. After adjusting for AF, the association between PA and AA disappeared while the association of AF with AA still remained. However, neither PA nor AF was associated with the AA of girls. Therefore, the hypothesis that AF might mediate the relationship between PA and AA was supported for boys. Promoting AF, as a result of engaging to PA could positively influence AA particularly in boys.