Background Men who have sex with men (MSM) and transgender women (TGW) are disproportionally affected by HIV infection in Latin America. This study aims to assess pre-exposure prophylaxis (PrEP) preferences among sexual and gender minorities (SGM) and identify attributes and levels that are related to PrEP uptake and adherence, both crucial for PrEP success. Methods We conducted a discrete choice experiment (DCE) among SGM from all Brazilian regions (September–December/2020). The survey was administered face-to-face (five Brazilian capitals) and online (entire country). We used a D-efficient zero-prior blocked experimental design to select 60 paired-profile DCE choice tasks. Findings The total sample size was 3924 (90.5% MSM; 7.2% TGW and 2.3% non-binary or gender diverse persons). In random-effects logit models, highest levels of protection and “no side effects” were the most important attribute levels. For “presentation”, injectable and implant were preferred over oral. Participants were willing to accept a 4.1% protection reduction to receive injectable PrEP or a 4.2% reduction if PrEP were taken monthly. The largest class in the latent class models was defined predominantly by the preference for the highest HIV protection level (p < 0.005). Respondents in this class also preferred no side effects, injectable and implant presentations. Interpretation Higher HIV protection, no side effects, and presentation, whether injectable or implant, were the most important attributes in PrEP preferences. Protection against HIV was the most important attribute. PrEP programs should make available technologies such as long-acting presentations that could reunite the most desired attributes, thus maximizing acceptability and user-appropriateness.