Background The injury burden in rugby union ('rugby') is high. While exercise-based injury prevention programmes have successfully reduced injuries in other sports such as football, there is minimal research on this topic in rugby union. Objective To evaluate the effectiveness and implementation of an exercise-based intervention (BokSmart Safe Six) in junior rugby players that aims to reduce the injury risk profile and burden of injury. Setting 14-16-year-old junior rugby players in two geographically separated locations in South Africa over the 2017 rugby playing season. Methods A cluster-randomised controlled trial where the teams are allocated to groups that either (1) have a coach-delivered exercise intervention in their warmup (BokSmart Safe Six) or (2) continue with their warm-up 'as usual' (control group). Injury risk profiles will be assessed through musculoskeletal screening on all players performed at the beginning, middle and end of the trial. Epidemiological measurements include injury surveillance at all matches and training sessions, and exposure to the various warm-up exercises (including BokSmart Safe Six exercises). Behavioural determinants of coaches will be assessed through standardised theory of planned behaviour questionnaires and focus groups before and after the intervention. Outcome measures Comparison in injury risk profiles and burden of injury between the intervention and control groups. Changes in the behavioural determinants of coaches.