IntroductionKey populations (KPs) including female sex workers (FSWs) and men who have sex with men (MSM) in sub‐Saharan Africa are disproportionately impacted by HIV. Despite the increasing availability of pre‐exposure prophylaxis (PrEP), data on retention remain limited. This study assessed PrEP retention at 1 and 12 months among Rwandan FSWs and MSM.MethodsWe analysed routine clinical data on adult FSWs and MSM receiving PrEP care from 11 health facilities in Kigali, Rwanda between 2019 and 2022. Retention was defined as attendance at regularly scheduled appointments for a PrEP refill. We used logistic regression to assess associations between demographic and clinical characteristics and retention at 1 and 12 months.ResultsAmong 2043 PrEP initiators, 1343 (66%) were FSWs and 700 (34%) were MSM. FSWs reported a median number of eight sexual partners in the prior 7 days, 70% reported condomless sex and 94% considered themselves at high HIV risk. About 1239 (92%) and 1032 (77%) were retained at 1 and 12 months, respectively. One‐month retention was lower among FSWs living with others (OR 0.59, 95% CI: 0.35−0.99; ref: living alone) or with low HIV risk perception (OR 0.12, 95% CI: 0.04−0.29). At 12 months, low HIV risk perception remained statistically significant (aOR 0.20, 95% CI: 0.12−0.32). At PrEP initiation, MSM reported a median of four sexual partners in the prior 12 months, 88% reported condomless sex and 72% considered themselves at high HIV risk. Retention rates were 96% at 1 month and 82% at 12 months. At 1 month, retention was higher among MSM with some education (OR 12.74, 95% CI: 2.74−70.93; ref: no education). At 12 months, retention was lower among MSM with part‐time employment (aOR 0.29, 95% CI: 0.11, 0.76), students (aOR 0.12, 95% CI: 0.04, 0.37) and unemployed (aOR 0.12, 95% CI: 0.05, 0.28); ref: full‐employed) and those unaware of PrEP at baseline (aOR 0.15, 95% CI: 0.10, 0.23).ConclusionsWe observed very high rates of PrEP retention among Rwandan FSWs and MSM. Predictors of retention included living situation, employment status, HIV risk perception and low PrEP awareness, but differed between FSWs and MSM. These findings suggest that targeted awareness campaigns tailored to different KPs could improve PrEP retention in care.