This study assessed drug use patterns among men who have sex with men (MSM) in Japan, and evaluated their potential associations with sexual risk behaviours. Between September and October 2016, study subjects were recruited through a cross-sectional survey (LASH: Love Life and Sexual Health) using a geosocial networking application for MSM. Of the participants, 25.4% (1756/6921) reported ever having used drugs, and 11.3% (780/6921) reported having done so in the past six months. Those who used drugs were more likely to have greater knowledge of HIV/sexually transmitted infections (STIs). Drug use in the past six months was independently associated with each of the following sexual risk behaviours in the same period: (i) six or more sexual partners (adjusted odds ratio [aOR] = 2.70, 95% confidence interval [CI]: 2.30–3.17); (ii) condomless anal intercourse (aOR = 2.88, 95% CI: 2.43–3.42); (iii) group sex (aOR = 2.60, 95% CI: 2.22–3.05); and (iv) sex work (aOR = 2.30, 95% CI: 1.67–3.16). These results suggest that MSM in Japan who use drugs are more likely to report sexual risk behaviours, while also having greater knowledge of HIV/STIs. Supporting MSM to minimise the harm from drug use may be helpful in reducing HIV transmission among this priority population.