Physical exercise offers health benefits for individuals with autism spectrum disorder (ASD). However, the literature on recommendations for exercise prescription is still limited. This study aims to identify the most beneficial type of exercise program and present the most effective guidelines for its prescription in individuals with ASD. A systematic review was carried out using the ERIC, Web of Science, PsycINFO, PubMed and Scopus databases in accordance with the PRISMA guidelines. Of a total of 1114 studies, 18 were considered eligible. Overall, the type of programs included aerobic exercise sessions with an average duration of 12 weeks, with 3 weekly sessions of 45 to 60 min. The assessment included the shuttle test protocol, the progressive cardiovascular endurance running protocol and the modified Bruce protocol. For the muscle strength exercises, the sessions lasted an average of 12 weeks, with 2 weekly sessions of 10 to 20 min, including 2 to 4 exercises, 1 to 3 sets, with 6 to 12 repetitions. The assessments included the handgrip strength test, the modified curve-up test and the push-up test. The programs had positive effects on cardiorespiratory capacity and hemodynamics, indicating that the benefits of training increase when both capacities are combined. This study provides useful guidelines for adapted sports coaches to prescribe exercise programs aimed at promoting quality of life in individuals with ASD.