Female sex workers (FSW) are affected by individual, network, and structural risks, making them vulnerable to poor health and well-being. HIV prevention strategies and local community-based programs can rely on estimates of the number of FSW to plan and implement differentiated HIV prevention and treatment services. However, there are limited systematic assessments of the number of FSW in countries across sub-Saharan Africa to facilitate the identification of prevention and treatment gaps. Here we provide estimated population sizes of FSW and the corresponding uncertainties for almost all sub-national areas in sub-Saharan Africa. We first performed a literature review of FSW size estimates and then developed a Bayesian hierarchical model to synthesize these size estimates, resolving competing size estimates in the same area and producing estimates in areas without any data. We estimated that there are 2.5 million (95% uncertainty interval 1.9 to 3.1) FSW aged 15 to 49 in sub-Saharan Africa. This represents a proportion as percent of all women of childbearing age of 1.1% (95% uncertainty interval 0.8 to 1.3%). The analyses further revealed substantial differences between the proportions of FSW among adult females at the sub-national level and studied the relationship between these heterogeneities and many predictors. Ultimately, achieving the vision of no new HIV infections by 2030 necessitates dramatic improvements in our delivery of evidence-based services for sex workers across sub-Saharan Africa.