Considerable evidence has shown that physical exercise could be an effective treatment in reducing stereotypical autism spectrum disorder (ASD) behaviors in children. The present study seeks to examine the underlying mechanism by considering the theoretical operant nature of stereotypy. Children with ASD (n = 30) who exhibited hand-flapping and body-rocking stereotypies were asked to participate in both control (story-time) and experimental (ball-tapping-exercise intervention) conditions. The experimental condition comprised 15 min of ball tapping during which the children were asked to tap a plastic ball as many times as they could. Results indicated that hand-flapping stereotypy was significantly reduced but body-rocking stereotypy following the ball-tapping-exercise intervention was not. These results not only confirm the positive impact of exercise intervention on stereotypic behavior as shown in many previous studies, but further suggest that physical exercise should be matched with the biomechanics of stereotypy to produce a desirable behavioral benefit.