Half of new HIV infections in Thailand are among young people, the majority of whom are young gay and other men who have sex with men (YMSM) and young transgender women (YTGW). Amid low pre-exposure prophylaxis (PrEP) coverage, we explored practice-based factors that impact PrEP engagement among YMSM and YTGW. In 2018, we conducted 4 focus group discussions with 20 YMSM and 5 YTGW, and 22 in-depth interviews (5 in 2022) with healthcare providers (HCPs), community-based organization (CBO)/nongovernmental organization (NGO) staff, and peer educators. The inclusion of PrEP in universal healthcare coverage, including YMSM and YTGW, is a substantial facilitator of PrEP use; however, systemic barriers at microsocial (lack of communication about PrEP from HCPs, teachers, parents), mesosocial (healthcare-service fragmentation, lack of PrEP-competent HCPs), and macrosocial levels (annual quotas on free HIV-testing, HIV- and sexual-stigma) constrain and disincentivize adolescents’ engagement with PrEP. National scale-up of youth-friendly and LGBT-affirmative CBO/NGO clinics, HCP training, and tailored programs to support adolescents’ adherence may promote PrEP engagement among YMSM and YTGW in Thailand.