Clinical and research interest is growing in mental health support for elite athletes, based on findings from epidemiological surveys conducted in Australia, the United States, and European countries. However, little is known about the mental health status of elite athletes in Asia, including Japan. In the current study, we examine the prevalence of mental health problems and suicidal ideation and its risk factors in Japan Rugby Top League players. We analyze anonymous web-based self-reported data from 251 currently competing Japan Rugby Top League male players. During the off-season from December 2019 to January 2020, data on anxiety and depression symptoms were collected using the Japanese version of the 6-item Kessler-6. Suicidal ideation was assessed using the Baron Depression Screener for Athletes. Among the players, 81 players (32.3%) had experienced symptoms of mild anxiety and depression during the previous 30 days, while 12 (4.8%) and 13 (5.2%) had suffered from moderate and severe symptoms, respectively. Nineteen athletes (7.6%) reported that they had experienced suicidal ideation during the previous 2 weeks. Players with mental health problems experienced more events in competitions and daily life, including reduced subjective performance, missing opportunities to play during the last season, changes in health condition, and thinking about a career after retirement, compared with players without such problems. Mental health issues in Japan Rugby Top League players, as elite athletes, may be common, and research and practice development is expected in the near future.