Problems with emotion regulation and behavior are often reported in children with autism spectrum disorders (ASD). This pilot study examined the effect of physical exercise on emotion regulation and behavioral functioning in children with ASD. Twenty-seven children aged 8-12 years were randomized into either an exercise intervention group (n = 15) or a control group (n = 12). The intervention group received a 12-week jogging intervention. Children's parents completed the Emotion Regulation Checklist and the Child Behavior Checklist pre- and post-intervention. The intervention group demonstrated significant improvement in emotion regulation and reduction in behavioral problems (ps < 0.05). Future studies should explore the mechanisms underlying the effects of physical exercise on emotion regulation and behavior in children with ASD.