Objective: The present study was aimed at analyzing the effect of physical activity on motor coordination in children with ASD. Methods: On 28 June 2021, a systematic review with meta-analysis was performed using the following databases: MEDLINE, SciELO, LILACS, PEDro, SPORTDiscus, CINAHL, SCOPUS, Web of Science, Cochrane, and Science Direct. We analyzed the methodological quality and risk of bias using the Jadad scale and Cochrane tool, respectively. Motor coordination results were meta-analyzed using the RevMan program. Two independent researchers used the Grading of Recommendations Assessment, Development, and Evaluation (GRADE) tool to assess the level of evidence from the meta-analysis. Results: We found four studies in the listed databases and five randomized clinical trials were included in the meta-analysis that included 109 children with ASD. Children with ASD who performed physical activity did not present significantly better motor coordination than control children (p = 0.12). Conclusions: Considering the clinical importance of physical activity for children with ASD, this systematic review with meta-analysis showed that physical activity had no statistically significant effects on coordination in individuals with ASD.