Difficulty with communication and social functioning are two outstanding core symptoms of autism spectrum disorder, and physical activity has long been suggested to improve autism spectrum disorder symptoms. In this meta-analysis of controlled trials, we examined the effects of physical activity interventions compared to controls on communication and social functioning in autistic children and adolescents. Included studies are published articles in English with autism spectrum disorder participants younger than 18 years. Literature search was conducted on MEDLINE, Embase, CINAHL, and related databases through 6 May 2020. Quality of study was assessed with the Cochrane risk-of-bias tool regarding randomization, allocation concealment, blinding, attrition, and selective reporting. We included 12 controlled trials (N = 350) with communication outcomes (k = 8) and/or social functioning outcomes (k = 11). Results show small to moderate intervention benefits on communication (standardized mean change = 0.27, 95% confidence interval (0.06, 0.48)) and social functioning (standardized mean change = 0.39, 95% confidence interval (0.15, 0.63)), but the result for social functioning may be susceptible to publication bias. Better intervention outcomes are observed in younger participants, suggesting the importance of early participation. This study shows the benefits of physical activity interventions, and they could be considered a cost-effective means for autism spectrum disorder management in the future.