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Pre-exposure prophylaxis (PrEP) has the potential to transform HIV in young Black and Latinx sexual minority men (SMM) and transgender women (TW). Addressing low PrEP uptake in this population depends on the better understanding of barriers to PrEP use. This article uses an ecological framework to explore barriers to daily oral PrEP in a sample of young Black and Latinx SMM and TW in three geographically prioritized cities in the United States. In-depth interviews were completed with 33 young Black and Latinx SMM and TW (22 at risk for and 11 recently diagnosed with HIV), aged 17-24, participating in a randomized trial aimed at increasing PrEP and antiretroviral therapy (ART) uptake and adherence. Interviews were recorded and transcribed, and then analyzed using inductive and deductive coding. Coded transcripts were organized into individual, interpersonal, community, and structural categories, by PrEP use and HIV status. Among participants, nine reported having been prescribed PrEP, with five actively or recently taking PrEP, whereas only one participant diagnosed with HIV had been prescribed PrEP. Major themes related to barriers emerged across the individual, family, community, and structural level. Limited barriers related to partners, instead partners with HIV encouraged PrEP use. Participants commonly reported low perceived HIV risk, fear of disclosure, barriers relating to insurance/cost, and medication use as reasons for nonuse of PrEP. For youth to remain on a healthy life course, HIV preventative measures will need to be adopted early in adolescence for those at risk of HIV acquisition. Interventions need to simultaneously address multilevel barriers that contribute to nonuse in adolescents. Clinical trials registry site and number: ClinicalTrials.gov Identifier: NCT03194477.