This study has examined the effect of after-school physical activity on body composition and health related fitness of middle school students. The duration of after-school physical activity training program of this study is 12 weeks, the training time in 1 hours warming-up 10 minutes, the skill training 45 minutes and cool down did in 5 minutes. Exercise frequency is 5 time per week. Height basketball class, soccer class, subject class showed statistically meaningful increase between group variance showed statistically meaningful. Weight basketball class, soccer class, showed statistically meaningful decrease. Muscle mass basketball class showed statistically meaningful increase, soccer class showed statistically meaningful decrease. Cardiopulmonary basketball class, soccer class, showed statistically meaningful decrease. Explosive muscular strength basketball class, soccer class, showed statistically meaningful decrease. subject class showed statistically meaningful increase, between group variance showed statistically meaningful. Flexibility basketball class showed statistically meaningful increase, soccer class. Muscular strength basketball class, soccer class, subject class showed not statistically meaningful different.