Men who have sex with men (MSM) and Transgender Women (TGW) in Thailand contribute to more than half of all new HIV infections annually. This cross-sectional study describes epidemiologic profiles of these key populations (KP) in Key Population-led Test and Treat study. Baseline data were collected using self-administered questionnaires and HIV/STI testing from MSM and TGW aged ≥18 years enrolled in a cohort study in six community sites in Thailand between October 2015 and February 2016. Factors associated with HIV prevalence were determined by logistic regression. TGW in the cohorts had lower education and income levels than MSM. TGW also engaged in sex work more, though similar proportions between MSM and TGW reported to have multiple sexual partners and STI diagnosis at baseline. HIV prevalence was 15.0% for MSM and 8.8% for TGW in the cohorts. HIV prevalence among TGW was more associated with sociodemographic characteristics, whereas factors related to behavioral risks were determined to be associated with HIV prevalence among MSM. TGW and MSM in the cohorts also had high prevalence of STI. Key Population-driven HIV services are able to capture harder-to-reach key populations who are at heightened risk for HIV.