Introduction: Pre-exposure prophylaxis (PrEP) is an important and well-established prevention strategy for sexual acquisition of HIV. In Brazil, transgender women (TGW) and men who have sex with men (MSM) bear the largest burden among key populations. Little is known about preferences for PrEP characteristics in these vulnerable populations in Latin America. The goal of this study is to investigate preferences of TGW and MSM with respect to PrEP characteristics, whether current user or not, and to assess any attributes and levels that may improve the decision to start using PrEP (uptake) and optimal continuity of use (adherence), which are important dimensions for PrEP success. Methods and analysis: We hereby outline the protocol of a discrete choice experiment (DCE) to be conducted among TGW and MSM in Brazil. The study will be carried out in two phases. The first phase involves literature review and qualitative approaches including in-depth interviews to inform the development of the DCE (attributes and levels). The second phase entails the DCE survey and supporting questions pertaining to sociodemographic and risk behaviour information. The survey is aimed at current PrEP users and non-users, consisting of two modes of administration: face to face in five Brazilian capitals (Rio de Janeiro, Brasília, Manaus, Porto Alegre and Salvador) and online targeting the entire country. A D-efficient zero-prior blocked experimental design will be used to select 60 paired-profile DCE choice tasks, in which participants will be randomly assigned to one of four groups and presented with a set of 15 choice tasks. The planned sample size is 1000 volunteers.