Background: To establish the 1-year prevalence of sports injuries and explore associations of various factors with a sports injury in Japanese collegiate athletes. Methods: The data were collected through a web-based survey of Japanese collegiate athletes associated with UNIVAS (Japan Association for University Athletics and Sport). The survey questions asked about athletes’ personal characteristics, sports participation, and injuries sustained within the previous year. Follow-up questions on the details regarding the three most serious injuries were asked. Differences in proportions of athlete characteristics between males and females and between injured and uninjured were explored with the chi-square test. Factors associated with sustaining an injury were determined with regression analysis. Results: The prevalence of injuries among Japanese collegiate athletes is high, and most of the sustained injuries require athletes to take a considerable time off training and competition indicating their severity. Athletes from year two and higher at the university, overweight or obese, training more often per week, and with longer sports experience were more likely to sustain an injury within the previous year. Conclusions: There is compelling evidence to suggest that excessive training and insufficient recovery may be contributing to their increased risk of injury. These findings underscore the importance of implementing evidence-based training programs and recovery strategies to mitigate injury risk and optimize performance outcomes among this population.