Adolescent men who have sex with men (AMSM) are at a heightened vulnerability for human immunodeficiency virus (HIV). This study aimed to estimate the prevalence of HIV and associated individual, social, and programmatic factors among AMSM in Salvador, Bahia State, Brazil. This is a cross-sectional study which analyzed baseline data from the PrEP1519 cohort in Salvador. Descriptive, bivariate, and multivariate analyses were conducted using the dimensions of vulnerability to HIV as hierarchical levels of analysis. Logistic regression models were used to estimate the odds ratios (OR) of the association between predictor variables and HIV infection. The prevalence of HIV infection among the 288 AMSM recruited to the project was 5.9% (95%CI: 3.7-9.3). Adjusted analysis showed a statistically significant association between self-identifying as a sex worker (OR = 3.74, 95%CI: 1.03-13.60) and HIV infection. Other associations with borderline statistical significance were the use of application programs to find sexual partners (OR = 3.30, 95%CI: 0.98-11.04), low schooling level (OR = 3.59, 95%CI: 0.96-13.41), failing to be hired or being dismissed from a job because of sexual orientation (OR = 2.88, 95%CI: 0.89-9.28), and not using health services as a usual source of care (OR = 3.14, 95%CI: 0.97-10.17). We found a high HIV prevalence among AMSM in Salvador. Furthermore, our study found that individual, social, and programmatic factors were associated with HIV infection among these AMSM. We recommend intensifying HIV combined-prevention activities for AMSM.