HIV incidence is disproportionately high among young cisgender men who have sex with men (YMSM), but YMSM are less likely than adults to use HIV pre-exposure prophylaxis (PrEP). Among YMSM living with HIV, peer navigation programs have been effective in linkage to care and increasing medication adherence; such programs may aid HIV-uninfected YMSM in overcoming barriers to engagement in PrEP care. We conducted 32 semi-structured qualitative interviews at a community health center in Massachusetts, USA, specializing in sexual and gender minority health with four sub-groups of YMSM who: (1) had never discussed PrEP with a medical provider, (2) had discussed PrEP with a medical provider but declined a prescription, (3) were prescribed PrEP and have sub-optimal adherence (taking fewer than 4 pills per week), and (4) were prescribed PrEP and were optimally adherent. Domains addressed in the interviews included knowledge of PrEP and HIV prevention, barriers and facilitators to PrEP adherence, and attitudes toward peer navigation for PrEP. Interviews were transcribed and coded using thematic analysis methodology. Multiple themes emerged from the interviews, including finding that perceived costs, anticipated stigma, sexual activity, and relationship status influence PrEP uptake and adherence; establishing pill-taking routines is an important adherence facilitator; and peer navigators could offer benefits for PrEP adherence.