In this article, we describe a community-based research (CBR) approach to making a national online survey of gay, bisexual, and other men who have sex with men (GBMSM) inclusive of transgender GBMSM by working with members of the transgender community at all stages of the research process. This collaboration resulted in 209 transgender GBMSM completing our survey and we contrasted their health experiences with 7439 cisgender GBMSM. We found that transgender GBMSM were less likely than cisgender GBMSM to report intercourse without a condom (AOR 0.43; 95% CI: 0.28-0.66) and to have had an HIV test (AOR 0.64; 95% CI 0.49-0.85). Transgender GBMSM were more likely to report discrimination in the health care system in their lifetime (AOR 4.17; 95% CI 3.03-5.73), to self-rate their health as poor (AOR 3.47; 95% CI 2.52-4.80), and to have discussed depression (AOR 3.47; 95% CI 262-4.59) or anxiety (AOR 3.27; 95% CI 2.47-4.33) with a health care provider. Our experience highlights the feasibility of including transgender individuals in GBMSM research, while the results affirm the need for GBMSM health services to take into account the unique experiences of transgender GBMSM.