Background: Peer support is strongly associated with physical activity of adolescents. This study examined the efficacy of a YMCA-based, peer-guided exercise training programme for increasing health-related physical fitness among adolescents with intellectual disabilities. Materials and Methods: Adolescents with intellectual disabilities and typically developing peer partners provided reciprocal support during 1-h exercise sessions that included aerobic exercise, weight training and stretching activities. The programme was conducted 2 days/week for 15 weeks and pre- and post-test fitness testing was conducted. Results: Participants demonstrated significant improvements in curl-ups, 6-min walk and BMI. Exercise session attendance was high and participants typically completed all of the prescribed aerobic and stretching exercises, whereas weight training exercises were completed less consistently. Conclusions: This peer-guided model integrates social and instructional support for adolescents with intellectual disabilities and may encourage exercise participation in community settings.