Despite high HIV incidence among young black men who have sex with men (YBMSM), pre-exposure prophylaxis (PrEP) uptake in this group is low. In a cohort of HIV-negative YBMSM in Atlanta, GA, all participants were offered PrEP as standard of care with free clinician visits and laboratory testing. We explored self-perceived need for PrEP among 29 in-depth interview participants by asking about reasons for PrEP uptake or refusal and factors that may lead to future reconsideration. Self-perceived need was compared to US Center for Disease Control and Prevention guidance for clinical PrEP indication using behavioral data and laboratory testing data. Self-perceived need for PrEP consistently underestimated clinical indication, primarily due to optimism for choosing other HIV prevention strategies, such as condom use, abstinence, or monogamy. Many participants cited consistent condom use and lack of sexual activity as reasons for not starting PrEP; however, follow-up survey data frequently demonstrated low condom use and high levels of sexual activity in the period after the interview. Study participants endorsed perceptions that PrEP is only for people with very high levels of sexual activity. Only one participant perceived incident sexually transmitted infection (STI) to be an indication for PrEP, despite the fact that several of the participants had a history of an STI diagnosis. These findings point to an opportunity for clinician intervention at diagnosis. Disconnect between self-perceived and guidance-based PrEP indications, as well as other factors such as medical mistrust or difficulty with access, may contribute to low PrEP uptake among YBMSM. A better understanding of the ways in which these issues manifest may be one tool for clinicians to support PrEP uptake.