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This study aimed to explore the effects of physical activity (PA) on motor skills and stereotypical behavior in children with autism spectrum disorder (ASD). Studies were searched in PubMed, Web of Science, Embase, the Cochrane Library, and CNKI. A total of 14 studies with 345 participants were included in this study, and a random-effects model with the standard mean difference (SMD) was used to calculate the effect size. We include 6 scales to evaluate motor skills and 2 scales to evaluate stereotyped behavior. Compared with the baseline, the PA group showed a significantly improved Test of Gross Motor Skills (TGMD) [SMD = 1.90 (95%CI: 0.78 to 3.02), p < 0.001] and Brininx-Oresetsky Test (BOT) [SMD = 7.37 (95%CI: 1.72 to 13.02), p = 0.01], while the control group did not significantly change in TGMD. For stereotyped behavior, there was a significant reduction in GARS-2 [SMD = −0.64 (95%CI: −1.10 to −0.18), p = 0.01] in the PA group compared with the baseline, while the control group did not significantly change. This meta-analysis confirmed the beneficial effects of PA on motor skills and stereotyped behavior in children with ASD. Engaging in activities like ball games at moderate intensity can be beneficial. Further research should examine the specific effects of various PA types and intensities to enhance PA-based interventions for ASD. • The core disorders of autism spectrum disorder (ASD) are low motor skills, stereotyped behaviors, and impaired social skills. • Low motor skills in children with ASD may be related to stereotyped behavior and developmental abnormalities. • Stereotyped behavior may have a negative impact on motor skill development in children with autism. • Physical exercise can effectively improve the motor skills and stereotyped behaviors of autistic children. [ABSTRACT FROM AUTHOR]