The purpose of this study was to describe the incidence, severity, and burden of injuries in Japanese male collegiate rugby union players. Initially, 170 male collegiate rugby union players from one university club were registered in this epidemiological surveillance study. The occurrence of injuries was recorded by a team medical staff during the 2017–2021 playing seasons. The incidence of injuries was 6.87 injuries/1000 h. This incidence was significantly higher during matches (100.37 injuries/1000 h) than that during training (3.63 injuries/1000 h). The severity of injuries was 31.0 days, and there were no significant differences between matches and training, or forwards and backs. The burden of injuries was 213.1 days/1000 h. This burden was significantly higher during matches (2887.8 days/1000 h) compared to training (120.1 days/1000 h). Matches had higher incidence of ankle sprain/ligament injuries (15.80 injuries/1000 h) and concussion (15.36 injuries/1000 h). The most common injury site was the ankle (1.24 injuries/1000 h). However, the greatest severity and burden were observed for knee injuries (severity: 59.1 days, burden: 48.6 days/1000 h). Furthermore, the greatest burden of injury type was knee sprain/ligament injuries (39.4 days/1000 h). In addition, the incidence of acromioclavicular joint injury was significantly higher in forwards, whereas hamstring strain was significantly higher in backs. The common injury mechanisms identified were being tackled (16.0%) and tackling (14.7%), followed by overuse (12.1%). In order to improve the player welfare of the Japanese collegiate rugby union players, it is necessary to work on the prevention strategy considering the injury profile.