Athlete well-being and mental health have become global priorities in high-performance sport. This study examined well-being and mental health symptoms among Japanese high-performance athletes and explored associations with psychological inflexibility, social support, and help-seeking attitudes. A total of 474 athletes (aged ≥ 16 years, across 42 sports) who had competed in recent Olympic or Paralympic Games or were national-team athletes completed self-report questionnaires. Overall, well-being was generally high; however, some athletes screened above clinical cutoffs for depression (9.9%), anxiety (8.4%), and insomnia (28.7%). The estimated prevalence of eating disorders was 5.4%. Psychological inflexibility was significantly associated with lower well-being and perceived performance, as well as higher levels of depression, anxiety, insomnia, suicidal ideation, and eating-disorder symptoms. These findings highlight that promoting psychological flexibility and strengthening culturally sensitive help-seeking are central to improving athlete well-being and mental health in Japan.