Introduction: Low bone mineral density (BMD) is a frequent issue in children and adolescents with inflammatory bowel disease (IBD). Several studies in healthy populations have reported a positive impact of physical activity (PA) on bone health. Recently, an observational study in paediatric patients with IBD showed a significant positive relationship between daily PA and BMD. However, intervention studies investigating a causal relationship between PA and BMD are warranted to confirm these results. The aim of this randomised controlled trial will be to investigate the effect of a PA programme on BMD in paediatric patients with IBD. Methods and analysis: This trial is a multicentre (four centres), randomised, controlled, blinded end-point study. Eighty children with IBD will be randomly assigned in a 1:1 ratio to receive a programme with adapted physical exercises (intervention group) or usual PA (control group) during a 9-month period. The primary outcome is the change from baseline at 9 months (the end of the study) in whole-body BMD assessed by dual-energy X-ray absorptiometry. Secondary efficacy outcomes include the changes from baseline at 9 months in: BMD assessed in the lumbar spine and trochanter; daily PA (time spent in moderate-to-vigorous PA); body composition (fat mass and fat-free mass); fatigue resistance; quality of life and activity of IBD. Ethics and dissemination: The study was approved by the Research Ethics Committee in France (Comité de Protection des Personnes, Sud-Ouest and Outre-Mer III, Bordeaux, France, No 2018/27). All procedures will be performed according to the ethical standards of the Helsinki Declaration of 1975, as revised in 2008, and the European Union's Guidelines for Good Clinical Practice. Written informed consent will be obtained from the parents or legal guardian and from the children. Research findings will be disseminated in peer-reviewed journals and scientific meetings. NCT03774329.