Despite the disproportionate burden of HIV facing transgender youth, they continue to be under-represented in studies designed to provide an empirical basis for pre-exposure prophylaxis (PrEP) programs that can meet the unique needs of this population. This study examined facilitators and barriers to participation in a PrEP adherence study. Ninety transgender male (TM) and 60 transgender female (TF) 14 – 21 year olds attracted to cisgender male sexual partners completed an online survey to examine (a) gender identity, age and family disclosure; (b) sexual experience, HIV/STI testing history and perceptions of HIV risk; (c) prior health services and (d) perceived PrEP research risks and benefits (e) and the relationship of these factors to the likelihood of study participation. Approximately 50% were likely to participate in the PrEP study. Participation facilitators included prior sexual and health service experiences (i.e. number of sexual partners, STI testing history, comfort discussing sexual orientation and HIV protection with health providers) and study access to PrEP and health services (i.e. daily HIV protection, not having to rely on a partner for protection, regular health check ups). Participation barriers included lack of concern about HIV, potential medication side effects, the logistics of quarterly meetings, remembering to take PrEP daily and reluctance to discuss gender identity with study staff. Requiring guardian consent was a participation barrier for youth under 18. Results suggest that successful recruitment and retention of transgender youth in PrEP prevention studies warrant protocols designed to address youth's underestimation of HIV risk, concerns regarding medical risk and study logistics, and their need for gender and sexual orientation affirming health services.