This study examined the effects of a 12-week physical activity intervention on the motor skill proficiency and executive function of 22 boys (aged 9.08 ± 1.75 years) with autism spectrum disorder. In Phase I of the 12 weeks, 11 boys with autism spectrum disorder (Group A) received the intervention, whereas the other 11 boys with autism spectrum disorder (Group B) did not (true control, no intervention). The arrangement was reversed in Phase II, which lasted an additional 12 weeks. The Bruininks–Oseretsky Test of Motor Proficiency, Second Edition, and the Wisconsin Card Sorting Test were conducted three times for each participant (Group A, primary grouping: baseline (T1), post-assessment (T2), and follow-up assessment (T3); Group B, control grouping: T1–T2; intervention condition, T2–T3). The main findings were that both groups of children with autism spectrum disorder significantly exhibited improvements in motor skill proficiency (the total motor composite and two motor-area composites) and executive function (three indices of the Wisconsin Card Sorting Test) after 12 weeks of physical activity intervention. In addition, the effectiveness appeared to have been sustained for at least 12 weeks in Group A. The findings provide supporting evidence that physical activity interventions involving table tennis training may be a viable therapeutic option for treating children with autism spectrum disorder.