Understanding the factors associated with pre-exposure prophylaxis (PrEP) adherence may help in the development of strategies to support, motivate and sustain PrEP use. This study estimated self-reported adherence, described perceived barriers and facilitators and investigated factors associated with adherence to daily oral PrEP among men who have sex with man (MSM) and transgender women after 1 year of PrEP use in Brazil. PrEP Brasil was a prospective, multicentre, open-label demonstration study with MSM and transgender women at high risk for HIV infection. We used logistic regression to evaluate factors associated with complete adherence (not forgetting to take any pills in the past 30 days) at week 48. Of 338 participants included in this analysis, 60% reported complete adherence to daily oral PrEP at week 48. Perceived barriers and facilitators to daily oral PrEP were reported by 38.2% and 98.5%, respectively. The most reported barrier and facilitator were 'I forgot to take my pills' (19.2%) and 'Associate PrEP with a daily activity/task' (58.6%), respectively. In final multivariable analysis, living in Rio de Janeiro (aOR: 0.38; 95% CI: 0.20-0.73), being transgender women (aOR: 0.22; 95% CI: 0.07-0.73), reporting stimulant use (a OR: 0.40; 95% CI: 0.20-0.80) and having any perceived barriers to daily oral PrEP (aOR: 0.12; 95% CI: 0.07-0.23) were associated with decreased odds of complete adherence. Our findings provide information for developing the best practices to promote PrEP adherence in the Brazilian context.