Background Basketball is one of the most played sports in the world. However, only a few studies have examined the epidemiology of Japanese collegiate men's basketball injuries. This study investigated the incidence of injury among Japanese collegiate men's basketball from the 2013/2014 to the 2019/2020 seasons and identified unique patterns by comparing our data with the National Collegiate Athletic Association (NCAA) men's basketball data. Methods Data from Japanese collegiate basketball teams of the Kanto Collegiate Basketball Federation Division I League during the 2013/2014 to 2019/2020 academic years (23 team-seasons) were used in this study. Injury rates per 1000 athlete exposures (AEs), injury proportions, and the injury rate ratio (IRR) were calculated according to the events, injury types, body parts, and common injury mechanisms. Injury rates were then compared with that from the time-loss injury data of the NCAA's previous reports. Results In total, 480 injuries during 97,515 AEs were reported, leading to an injury rate of 4.92 per 1000 AEs (95% CI = 4.48-5.36). The overall injury rate was higher in Japan than in the NCAA ([2009/2010-2014/2015] IRR = 1.55, 95% CI = 1.39-1.73; [2014/2015-2018/2019] IRR = 1.64, 95% CI = 1.48-1.82). Lower extremity injuries occurred most frequently (73.5%). Ankle sprain was the most common injury in Japan, with higher injury rates than in the NCAA (IRR = 2.10; 95% CI = 1.72-2.57). The injury rate of concussion was lower in Japan than in the NCAA (IRR = 0.28; 95% CI = 0.14-0.55). Conclusions The rates of overall injury and ankle sprain were higher and that of concussion was lower in Japan than in the NCAA. These results suggested the existence of international differences in the pattern or features of injuries in basketball players.