Background The HIV continuum of care for men who have sex with men (MSM) in South Africa remains inadequately characterised, hindering the tracking of progress towards ending the HIV epidemic. We estimated HIV prevalence and care continuum indicators for MSM in three South African cities. Methods and findings MSM were recruited via respondent-driven sampling (RDS) methods in Cape Town, Johannesburg, and Mahikeng. Eligibility criteria included age ≥ 18 years, assigned male sex at birth, recent oral or anal sex with a man, and living, working, or socialising in one of the selected cities within the past six months. Participants completed a survey, and dried blood spots were collected to test for HIV antibodies, antiretrovirals, and HIV viral load. RDS weights were used to estimate HIV prevalence and 95-95-95 care continuum indicators. From May to October 2019, 1,790 cisgender MSM were sampled. HIV prevalence was highest in Johannesburg (weighted prevalence = 40.7%, 95% confidence interval 34.4–47.3), followed by Cape Town (25.2%, 20.9–30.1) and Mahikeng (14.7%, 12.0–17.8). Among MSM living with HIV, awareness of status was 67.0% (56.8–75.8) in Cape Town, 67.8% (56.7–77.1) in Johannesburg, and 60.2% (49.9–69.8) in Mahikeng. ART coverage among those aware of their status was 65.1% (53.4–75.2) in Cape Town, 77.9% (67.2–85.8) in Johannesburg, and 72.5% (58.6–83.0) in Mahikeng. Viral suppression among those on ART was 79.3% (59.5–90.9) in Cape Town, 88.7% (77.8–94.6) in Johannesburg, and 90.7% (78.1–96.4) in Mahikeng. Conclusions Achievements towards HIV care indicators were sub-optimal for MSM in three South African sites, revealing potential gaps in the reach and uptake of HIV testing and treatment services. Research identifying multi-level determinants of these gaps is needed to guide the development of contextually appropriate and effective interventions.