Background Data from high-income countries suggest increasing hepatitis C virus (HCV) prevalence/incidence among HIV-infected men who have sex with men (MSM), but limited data derive from low-and-middle-income countries (LMICs). Methods We recruited 4,994 MSM from 5 states across India using respondent-driven sampling (RDS). Logistic regression incorporating RDS weights and machine learning feature selection were used to identify correlates of prevalent HCV, and Bayesian phylogenetic analysis was used to examine genetic clustering. Results Median age was 25, HIV prevalence was 7.2% and 49.3% reported recent unprotected anal intercourse. HCV prevalence was 1.3% (95% CI: 1.0 – 1.6%; site range: 0.2 – 3.4%) and was 3.1% in HIV-positive compared to 1.1% among HIV-negative. HCV infection was significantly associated with injection drug use (OR: 177.1; 95% CI: 72.7 – 431.5) and HIV (OR: 4.34; 95% CI: 1.88 – 10.05). Machine learning did not uncover any additional epidemiologic signal. Phylogenetic analysis revealed three clusters suggestive of linked transmission; each contained at least one individual reporting injection drug use. Conclusions We observed a low HCV prevalence in this large sample of MSM despite high prevalence of known risk factors, reflecting either the need for a threshold of HCV for sexual transmission and/or variability in sexual practices across settings.