Selective eating and hyperphagia are frequently encountered in individuals with autism spectrum disorder (ASD). They may increase arterial stiffness, a risk factor for cardiovascular disease, via excessive sodium intake, nutritional deficiency, and obesity. Therefore, primary prevention of cardiovascular disease is an important issue in this population. To test our hypothesis that greater levels of physical activity are associated with lower levels of arterial stiffness in individuals with ASD as well as those without ASD, this study compared brachial-ankle pulse wave velocity (baPWV) in active males with and without ASD and less active males without ASD. We recruited subjects with ASD via organizations providing opportunities to play sports. Subjects without ASD were subdivided into less and more active groups based on scores from the International Physical Activity Questionnaire. Daily physical activity levels were higher in the more active control (2992 ± 681 MET min/week) and ASD (2992 ± 972 MET min/week) groups than in the less active control group (337 ± 86 MET min/week). BaPWV was lower in the more active control (10.7 ± 0.3 m/s) and ASD (9.9 ± 0.6 m/s) groups than in the less active control group (11.7 ± 0.3 m/s). There were no differences in physical activity level and baPWV between more active males with ASD and those without ASD. These results suggest that physically active males with ASD also have elastic central arteries. We would like to propose that participation in physical activities may be beneficial as a primary cardiovascular disease prevention strategy for not only for males without ASD but also those with ASD.