Objectives: Youth rugby union is a popular sport with a high injury incidence density (IID) and burden. This high risk has called for further research into the factors affecting the injuries in youth rugby. The aim of the study was to analyse time-loss IID and burden in multiple schoolboy rugby teams over a season and the potential factors associated with injury. Design: Prospective cohort Methods: All time-loss injuries were recorded from three schools for the whole season. Overall IID and injury burden were calculated, as well as for injury event, type, location and the match quarter in which they occurred and Poisson regression analyses were performed to determine differences. Results: IID was 28.8 (18.9–38.6) injuries per 1000 player hours over the season, with an injury burden of 379.2 (343.6–414.9) days lost per 1000 player hours. The ball-carrier had a significantly higher IID (11.3 (5.2–17.5) per 1000 player hours) compared to other events, and the joint (non-bone)/ligament injuries were the most common (IID of 12.2 (5.8–18.6) per 1000 player hours) and severe type of injury (burden of 172.6 (148.5–196.6) days lost per 1000 player hours). Conclusions: The IID was similar to previous youth rugby studies, however the injury burden was much lower. The South African youth cohort showed similar factors associated with injury for inciting event (the tackle) and injury type (joint (non-bone)/ligament) and location (lower limb) as seen in other studies in both youth and senior players.