Introduction Transgender persons experience health disparities and are marginalized in many societies worldwide. Even their numbers are unknown in many countries. We conducted the first effort to estimate the population size of transgender women (TGW) and transgender men (TGM) in Bhutan from November 2019 to January 2020. Methods Community-based surveys of TGW and TGM integrated several methods to estimate the size of hidden populations, including key informant mapping, wisdom-of-the-crowd, the service multiplier, and the unique object multiplier. Results of the several methods were synthesized using a Bayesian approach. Results Surveys included 34 TGW and 124 TGM. TGW was persons assigned to the male sex at birth and currently self-identified as “trans women” (91%), “women” (6%), or another gender (3%). TGM were persons assigned female sex at birth and self-identified as “trans men” (100%). Bayesian synthesis of the multiple methods estimated 84 TGW (credible interval 61–110) and 166 TGM (credible interval 124–211) in Bhutan. Conclusions Our study documented that TGW and TGM are part of Bhutanese society, with TGW constituting 0.03% of adult women and TGM 0.06% of adult men. Estimates can help advocate for resources and programs to address the health and well-being of these communities.