This study aimed to explore the effect of family-professional partnerships in adapted physical education on the fundamental motor skills, physical activity levels, and adaptive behaviors of children with autism spectrum disorder (ASD) and on parental satisfaction. A randomized controlled trial design was used, with pre-and post-intervention evaluations. Participants (n = 40), including children with ASD and their parents, were divided into three groups: (a) a family-school group (FSG-A, n = 14), (b) a school group (SG-B, n = 13), and (c) a control group (CG-C, n = 13). After 12 weeks of intervention, the within-group comparison revealed that the FSG-A performed better than the SG-B and CG-C for all variables. The among-group comparison further revealed that the FSG-A had greater fundamental motor skill scores than the SG-B (p = 0.021) and CG-C (p < 0.001), had greater adaptive behavior and family-professional partnership scores than the SG-B and CG-C (p < 0.001 for all), and had higher physical activity levels than the SG-B (p < 0.05) and CG-C (p < 0.001). This study underscores the significance of robust family-professional partnerships in exercise interventions for children with ASD.