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Background and objective Reports on the mental health of Japanese athletes have been increasing in recent years, although many focus on specific sports, such as rugby. In this study, we hypothesized that the mental health of elite Japanese athletes was affected by the COVID-19 pandemic and the Tokyo 2020 Olympics, leading to a rise in mental health issues. The aim of this study was to clarify the impact of these events on the mental health of elite athletes and to identify trends and characteristics of those who sought care at the clinic. Methods We conducted a retrospective, cross-sectional observational study using medical records from the Sports Clinic at the Japan Institute of Sports Sciences (JISS), covering the period from January 1, 2019 to December 31, 2022. All athletes who received psychiatric or counseling services during this time were included. There were no exclusion criteria or age restrictions. Participant characteristics were analyzed using the chi-square test and Fisher's exact test for categorical variables and the Welch t-test for continuous variables. All tests were two-tailed, with a significance threshold set at p < 0.05. Results A total of 85 athletes (23 men and 62 women) received treatment during the study period. Most of the patients visiting the mental health department at the JISS Sports Clinic were female athletes involved in individual sports, particularly in record-oriented disciplines. Since the onset of the COVID-19 pandemic, the number of athletes seeking mental health support has increased significantly. Reasons for consultation included both psychological issues, such as sleep disorders, and physical symptoms, such as gastrointestinal problems. Conclusions Mental health issues among elite Japanese athletes often manifest as psychosomatic symptoms. Recognizing this pattern is important for sports physicians, especially those without psychiatric training, and can support the development of effective care systems tailored to athletes' needs.