HIV-related stigma is a pervasive structural driver of HIV. With an HIV epidemic among young men who have sex with men (MSM) and transgender women (TG) in Thailand characterized as explosive, we conducted a cross-sectional survey among MSM and TG aged 18–30 years. From April–August 2013, participants recruited using venue-based sampling from gay entertainment sites and community-based organizations completed a tablet-assisted survey interview in Thai language. We conducted multiple logistic regression to assess correlations between HIV-related stigma (felt-normative, vicarious domains) and socio-demographic variables, HIV vulnerabilities (gay entertainment employment, sex work, forced sex history), and HIV prevention uptake (condom use, HIV testing, rectal microbicide acceptability). Among participants (n = 408), 54% identified as gay, 25% transgender, and 21% heterosexual. Two-thirds (65.7%) were employed at gay entertainment venues, 67.0% had more than three male partners (past month), 55.6% had been paid for sex, and 4.5% were HIV-positive. One-fifth (21.3%) reported forced sex. Most participants reported experiencing felt-normative and vicarious HIV-related stigma. Adjusting for socio-demographics, participants with higher total HIV-related stigma scores had significantly lower odds of HIV testing and rectal microbicide acceptability, and higher odds of having experienced forced sex. Both vicarious and felt-normative dimensions of HIV-related stigma were inversely associated with HIV testing and rectal microbicide acceptability. Our findings suggest that HIV-related stigma harms the health of HIV-negative MSM and TG at high risk for HIV infection. HIV-related interventions and research among young MSM and TG in Thailand should address multiple dimensions of HIV-related stigma as a correlate of risk and a barrier to accessing prevention.