Little is known about accurate prevalence and associated factors of deliberate self-harm (DSH) among adolescents in Asian countries. In this study, the prevalence and associated factors of DSH among adolescents in Japan were examined. Data were derived from a cross-sectional survey using an anonymous self-report questionnaire and enrolling 8,620 adolescents aged 12-15 and 9,484 aged 15-18. DSH in the previous 12 months was reported by 3.3% (95% CI, 2.9-3.7) of junior and 4.3% (3.9%-4.7%) of senior high school respondents. The prevalence was more than four times as high among girls as among boys for both age groups. DSH was further strongly associated with having suicidal thoughts, having depression/anxiety symptoms, and having used recreational drugs. These associated factors were similar for both sexes and for both older and younger teenagers. A substantial minority of adolescents present with DSH, even among those aged 12-15. The prevalence of DSH in Japan was in the lower ranges of those reported for Western countries. The identified associated factors were not dissimilar from those reported in the West.