The purpose of this study was to examine factors hindering the use of mouthguards and the incidence of orofacial injury among young male rugby players. 69 high school rugby players (Group 1) and 431 medical student rugby players (Group 2) participated in this study. Participants in Group 1 used custom-made mouthguards fabricated according to a standardized method, whereas participants in Group 2 used custom-made or over-the-counter mouthguards of their choice. The factors associated with orofacial injury were assessed by logistic regression analysis, while factors hindering mouthguard use were assessed by multinomial logistic regression analysis. All data were obtained from a questionnaire developed by the Japanese Academy of Sports Dentistry. We found that breathing problems were the main factor contributing to the reduced frequency of mouthguard use. In both groups, a significant negative association was observed between the frequency of mouthguard use and the risk of orofacial injury. The group using standardized custom-made mouthguards reported fewer complaints about breathing problems and a higher frequency of mouthguard use. The results of this study suggest that increasing the frequency of mouthguard use would reduce the risk of orofacial injury among young male rugby players. We also conclude that users of custom-made mouthguards complain less frequently of breathing difficulties.