This study examined the prevalence and factors associated with inconsistent condom use among men who have sex with men (MSM) who use gay mobile geo-social networking applications (gay mobile apps) in Greater Tokyo. Among a sample of 1657 MSM recruited through advertisements on gay mobile apps, inconsistent condom use was reported by over one-third (37%) of participants with regular male partners, 18% with casual male partners, and 20% with female partners. In multiple regression analysis, inconsistent condom use with both regular and casual male partners was more commonly reported among participants without a university education, and among participants reporting lower self-efficacy for safer sex. Inconsistent condom use with casual male partners was more commonly reported among participants living in the central 23 wards of Tokyo. Inconsistent condom use with regular male partners was more commonly reported among participants who identified as a member of the gay community, and who only had male partners. These results indicate that a substantial proportion of Greater Tokyo gay mobile app users use condoms inconsistently, particularly with regular partners, and may be at risk for HIV. This paper provides useful information to help design tailored strategies to reduce inconsistent condom use.