An inverse association between socioeconomic status (SES) and mental health has been previously well reported, but the evidence is limited in Asian populations. We therefore investigated the association of SES and subjective mental health and prevalence of any mental disorders in the general population of Japan. We used data from the World Mental Health Japan Survey of 1,496 randomly selected people aged 20 years and older in Japan. Information on education level and household income were used as objective SES indicators, and subjective social status (SSS) was measured by responses to a question regarding social position. We calculated odds ratios of SES indicators for poor subjective mental health and 12-month prevalence of any mental disorders. The adjusted odds ratio (OR) (95 % confidence interval (CI)) of respondents who rated themselves as lower than middle status in the country (low SSS group) for poor subjective mental health was 2.24 (95 % CI: 1.41, 3.57) with reference to those who rated themselves as higher than middle status (high SSS group). Similarly, inverse associations of education level and household income with poor subjective mental health were identified. A J-shaped association was confirmed between SSS and 12-month prevalence of any mental disorders. The adjusted OR (95 % CI) of SSS for any mental diseases was 0.53 (95 % CI: 0.32, 0.86) for the middle SSS group and 1.61 (95 % CI: 0.96, 2.72) for the low SSS group, compared with the high SSS group. Those associations were not attenuated when objective SES indicators were adjusted. We found inversely linear associations between subjective and objective SES and poor subjective mental health among Japanese men and women. SSS was not significantly associated with 12-month prevalence of any mental disorders. Substantial social inequalities in mental health were identified in Japan, which has been considered an egalitarian society with relatively few inequalities in health.