In children and youth with disability, the risk of obesity is higher and is associated with lower levels of physical activity, inappropriate eating behaviors, and chronic health conditions. We determined the effectiveness of a program in managing weight, through changes in physical activity and nutrition behaviors in overweight and obese New Zealand children and youth with intellectual disability or autism. Twenty-two children and youth 14 plus or minus 4 y (mean plus or minus SD) and their families participated in a 10-week school-based program. The program consisted of 18 sessions focusing on physical activity and nutrition. Changes were measured immediately after completion of the program (post 1) and at 24 weeks (follow up). Fitness was assessed with the six-minute walk-test (6MWT) and body fatness via waist circumference and BMI. Physical activity and nutrition changes were measured by means of proxy reporting and interviews with parents. Individual interviews were conducted with school teachers and program leaders at 24 weeks to gain feedback regarding the program. Most quantitative outcomes were either unclear or trivial. The only possible change was observed in the six-minute walk-test where 24 weeks post program where participants walked 51 m further. There was however, a substantial reduction in the consumption of confectionery and chocolate at the two measurement points. Parents commented that during the program there were less hospital visits and absences from school related to illness. The program assisted in the development of a supportive community network and participants' abilities to partake in family and community activities. This the first study to report on the results of a physical activity and nutrition program targeted in children and youth with intellectual disability and autism. The results of this study may support and inform future developments of an integrated weight management and prevention program to enhance the health and well being in children and youth with disabilities. (Contains 6 tables.)