Background: Periodontal disease is prevalent among elite athletes globally, yet its status in Japanese athletes remains unclear. This study assessed periodontal risk in Japanese university athletes and its association with oral health-related quality of life (QOL), sports performance, and immune status. Methods: A cross-sectional study was conducted with 313 university athletes (basketball, volleyball, athletics). Periodontal risk was evaluated using a Trypsin-Like Peptidase activity assay (TLP-AA) kit; a score ≥ 1.5 indicated the presence of Red Complex bacteria (positive risk). Participants completed the Oral Impacts on Daily Performance (OIDP), Oslo Sports Trauma Research Centre (OSTRC) overuse injury, and Immune Status Questionnaires (ISQ). Results: Positive periodontal risk was identified in 25.9% (81/313) of athletes. While overall prevalence was not statistically different from the general population (17.8%), specific associations emerged. Positive risk was significantly associated with “pain related to sports” (OSTRC) overall (p = 0.016) and specifically in males (p = 0.004). Among track and field athletes, positive risk was associated with difficulty “smiling/laughing” (OIDP, p = 0.033) and lower self-rated general health (p = 0.032) and immune functioning (p = 0.047). Conclusions: Periodontal risk is notable in Japanese university athletes and is significantly associated with sports-related pain and specific QOL domains. Regular oral health monitoring may be crucial for maintaining athletic performance and well-being.