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Introduction: Developing effective targets, policies and services for key populations requires estimations of population sizes and HIV prevalence across countries and regions. We estimated the relative and absolute HIV prevalence among men who have sex with men (MSM), transgender women and men, and male and transgender sex workers (MSW and TGSW) in sub-Saharan African countries using peer-reviewed literature., Methods: We performed a systematic review of peer-reviewed studies assessing HIV prevalence in MSM, transgender women and men, MSW and TGSW in sub-Saharan Africa between 2010 and 2021, following PRISMA guidelines. We searched Embase, Medline Epub, Africa Index Medicus, Africa Journal Online, Web of Science and Google Scholar. We calculated HIV prevalence ratios (PRs) between the study prevalence, and the geospatial-, sex, time and age-matched general population prevalence. We extrapolated results for MSM and transgender women to estimate HIV prevalence and the number living with HIV for each country in sub-Saharan Africa using pooled review results, and regression approximations for countries with no peer-reviewed data., Results and Discussion: We found 44 articles assessing HIV prevalence in MSM, 10 in transgender women, five in MSW and zero in transgender men and TGSW. Prevalence among MSM and transgender women was significantly higher compared to the general population: PRs of 11.3 [CI: 9.9-12.9] for MSM and 8.1 [CI: 6.9-9.6] for transgender women in Western and Central Africa, and, respectively, 1.9 [CI: 1.7-2.0] and 2.1 [CI: 1.9-2.4] in Eastern and Southern Africa. Prevalence among MSW was significantly higher in both Nigeria (PR: 12.4 [CI: 7.3-21.0]) and Kenya (PR: 8.6 [CI: 4.6-15.6]). Extrapolating our findings for MSM and transgender women resulted in an estimated HIV prevalence of 15% or higher for about 60% of all sub-Saharan African countries for MSM, and for all but two countries for transgender women., Conclusions: HIV prevalence among MSM and transgender women throughout sub-Saharan Africa is alarmingly high. This high prevalence, coupled with the specific risks and vulnerabilities faced by these populations, highlights the urgent need for risk-group-tailored prevention and treatment interventions across the sub-continent. There is a clear gap in knowledge on HIV prevalence among transgender men, MSW and TGSW in sub-Saharan Africa., (© 2022 The Authors. Journal of the International AIDS Society published by John Wiley & Sons Ltd on behalf of the International AIDS Society.)