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Objectives To determine the effect on participation attendance (being there) and involvement (experience of participation) compared with usual activities of a community gym-based physical activity intervention ( FitSkills) for young people with disability.Methods An assessor-blinded stepped wedge cluster randomised trial was completed involving 163 participants with self-identified disability (61 female; mean age 19), 123 mentors and 11 sites randomised to four groups. Participant and mentor pairs exercised together two times a week for 12 weeks. The primary outcomes were participation attendance and involvement, and health-related quality of life measured by five questionnaires (Adolescent Physical Activity Recall; Adolescent Sedentary Activity; Children’s Assessment of Participation and Enjoyment; Participation and Environment Measure Children and Youth (PEM-CY); Child Health Utility 9D). The secondary outcomes were participation preferences, walking capacity, attitudes to exercise, physical activity and well-being (life satisfaction). Data were analysed using linear mixed-effects models.Results Immediately after the intervention, there was an increase in participation attendance, measured in terms of the number of different physical activities participated in (0.8 activities, 95% CI 0.4 to 1.1); and frequency (how often activities were performed) for one outcome, the PEM-CY (0.2 units, 95% CI 0.01 to 0.4). There was an increase in time spent doing physical activities (23%, 95% CI 4% to 46%), but no change in sedentary time (3%, 95% CI −6% to 12%). Analysis of time-averaged effects up to 15 months after the intervention showed an increase in the number of physical activities (1.0 activities, 95% CI 0.4 to 1.6) only. There was no change in the primary outcomes of participation involvement (ie, experience of participation) or health-related quality of life immediately after the intervention, or across time.Conclusion A student-mentored community-gym-based physical activity intervention increased self-reported physical activities in the intermediate term but did not change health-related quality of life in young people with disability.Trial registration ACTRN12617000766314.