Abstract Background: Evidence comparing functional training with traditional physical education in Chinese high schools is limited. This longitudinal study compared a 36-week functional training program versus standard physical education on fitness and health markers in male adolescents. Methods: Male adolescents (N = 670; aged 16–18 years) from 18 high schools were allocated to a functional training group (FTG, n = 351) or traditional physical education group (TPEG, n = 319).