Introduction While overweight and obesity in children and adolescents is a major global health problem, the effects of exercise on overweight and obesity in children and adolescents are not well established despite numerous studies on this topic. The purpose of this study is to use the network meta-analytic approach to determine the effects of exercise (aerobic, strength training or both) on body mass index (BMI) z-score in overweight and obese children and adolescents. Methods and analysis Randomised exercise intervention trials >4 weeks, published in any language between 1 January 1990 and 31 September 2015, and which include direct and/or indirect evidence, will be included. Studies will be retrieved by searching 6 electronic databases, cross-referencing and expert review. Dual abstraction of data will occur. The primary outcome will be changes in BMI z-score while the secondary outcome will be changes in body weight in kilograms (kg). Risk of bias will be assessed using the Cochrane risk of bias assessment instrument while confidence in the cumulative evidence will be assessed using the Grading of Recommendations Assessment, Development and Evaluation (GRADE) instrument for network meta-analysis. Network meta-analysis will be performed using multivariate random-effects meta-regression models. The surface under the cumulative ranking curve will be used to provide a hierarchy of exercise treatments (aerobic, strength training or both). Dissemination The results of this study will be presented at a professional conference and published in a peer-reviewed journal.