Autism spectrum disorder (ASD) is a neurodevelopmental disorder that is characterized by deficits in social communication, interaction, and stereotypical behaviours. Children with ASD have not enough opportunities to participate in physical activity (PA), which lead to increase fitness and health problem. The aim of this study was to compare two programs on motor skills. In the current investigation, 30 high functioning autistic children were diagnosed by a psychiatrist and randomly divided into control and experimental groups. The evaluation tools included the Brininx-Oresetsky Test (BOT) and a program named "I can have physical literacy" (ICPL) and Sport, Play, and Active Recreation for Kids (SPARK). The experimental intervention groups received sixteen sessions of 60 min, while the control group did not receive any treatment. Analysis of covariance was used to determine the difference between the groups. Post-hoc test was used to compare pairs of groups. Results showed that the experimental ICPL and Spark groups had increased motor skills (MS). There were significant differences between groups on gross motor skills. There were significant differences between the control and experimental ICPL groups, and between the experimental Spark and experimental ICPL groups. Both of these programs increased MS. ICPL program that address the characteristics of children with ASD, have a positive effect on their MS.