Children with autism exhibit more pronounced symptoms of both problem behaviors and motor coordination difficulties. Yoga, recognized as an effective intervention modality, can be valuable after assessing its efficacy in addressing problem behaviors and motor coordination challenges, ultimately contributing to symptom alleviation in autism. The randomized controlled trial (RCT) was used to divide 17 children with autism into an intervention group (n = 9) and a control group (n = 8). The intervention group participated in an 8-week yoga intervention training (three sessions/week, 45–50 min/session), and the control group did not participate in yoga training but only in daily program activities. Pre-test, mid-test, post-test, and after delayed test, teachers assessed the effect of yoga intervention on problem behaviors of children with autism through the Aberrant Behavior Checklist (ABC) and the effect of yoga intervention on motor coordination through the Movement Assessment Battery for Children—Second Edition (MABC2). Results show that the yoga intervention is effective in reducing problem behaviors and improving motor coordination in children with autism. Yoga intervention significantly reduces irritability and social withdrawal in children with autism. Yoga intervention had the most significant improvement in ball skills and static and dynamic balance.