High rates of heavy alcohol use among men who have sex with men (MSM) and transgender women (TW) have been linked to increased vulnerability for HIV and poor mental health. While theories explaining elevated drinking levels among sexual minorities have been forwarded, few investigations have assessed the potential pathways using empirical data, particularly with an explicit focus on self-stigma and among MSM and TW in low- and middle-income countries. This study examined the relationship between stigma-related stress (specifically, self-stigma and concealment of one's sexual orientation) and binge drinking in a sample of MSM and TW (n = 670) in San Salvador, El Salvador, recruited using respondent-driven sampling. Levels of alcohol consumption among participants were high: only 39 % of the sample did not drink alcohol or did not binge drink, while 34 % engaged in binge drinking at least weekly. Among MSM, high self-stigma was associated with binge drinking at least weekly (adjusted relative risk ratio (aRRR) = 2.1, p < 0.05). No such relationship was found with less than weekly binge drinking. Among both MSM and TW, having a female partner was associated with binge drinking less than weekly (aRRR = 3.3, p < 0.05) and binge drinking at least weekly (aRRR = 3.4, p < 0.05), while disclosure of sexual orientation to multiple types of people was associated with binge drinking less than weekly (aRRR = 2.9 for disclosure to one-two types of people, p < 0.01; aRRR = 4.0 for disclosure to three-nine types of people, p < 0.01). No such relationship was found with at least weekly binge drinking. Binge drinking at least weekly was marginally associated with a number of sexual health outcomes, including high number of lifetime partners (adjusted odds ratio (aOR) = 1.7, p < 0.10), inconsistent condom use with a non-regular partner (aOR = 0.5, p < 0.10), and decreased intention to test for HIV in the next 12 months (aOR = 0.6, p < 0.10). With the exception of inconsistent condom use with a non-regular partner (aOR = 0.4, p < 0.05), binge drinking less than weekly was not associated with increased sexual risk behavior and was actually associated with increased intention to test for HIV in the next 12 months (aOR = 2.8, p < 0.01). These findings support multiple pathways linking stigma-related stress to alcohol use. Specifically, those with high self-stigma and identity concealment may be using alcohol as a maladaptive coping and emotion regulation strategy, while those who have disclosed their sexual orientation to multiple types of people may be more engaged with the sexual minority community, likely in bars and other venues where permissive norms for alcohol use prevail. That this frequency of binge drinking does not appear to be associated with increased sexual risk behavior (and may even be associated with increased intention to test for HIV in the next 12 months) lends further support to the suggestion that these individuals with healthy concepts of the self (as indicated by high levels of disclosure and low levels of risky sexual behavior) may engage in binge drinking because of the influence of the social environment. Further research is needed to establish the pathways linking stigma-related stress to heavy alcohol use so that points of intervention can be identified.