This study adopted a quasi-experimental design to explore the effects of fundamental movement skill intervention on the acquisition and retention of physical activity levels and health-related fitness in children with autism spectrum disorder (ASD). In the experiments, 11 children received fundamental motor skill training (12 weeks, 60 min/session, 4 times/week), and 10 children maintained traditional physical activity. Assessments were performed using an ActiGraph GT3X+ accelerometer, health-related fitness pre–post intervention, and 1-month follow-up tests. The sedentary time during physical activity was significantly decreased (p = 0.01), and there were large changes in health-related physical fitness indicators, including significantly improved body composition (body mass index, F(1,19) = 8.631, p = 0.03, partial η2 = 0.312), muscle strength and endurance (sit-ups, F(1,19) = 3.376, p = 0.02, partial η2 = 0.151 and vertical jumps, F(1,19) = 5.309, p = 0.04, partial η2 = 0.218), and flexibility (sit and reach, F(1,19) = 36.228, p = 0.02, partial η2 = 0.656). Moreover, the follow-up tests showed that the children’s sedentary time continued to reduce, and the muscle strength and endurance (sit-ups, F(1,19) = 4.215, p = 0.01, partial η2 = 0.426) improved continuously after the intervention. Based on this study, actionable and regular fundamental movement skill programs can be provided in the future as an effective way to achieve the healthy development goals of children with ASD.