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Background The HIV epidemic remains an important public health challenge for the sub-Saharan region. Female Sex Workers (FSW) in this region are among the most vulnerable of the key population groups with HIV prevalence as high as twice that of the general population. The aim of this study was to estimate HIV prevalence and explore sexual risk behaviors among FSW in Togo. Methods A cross-sectional study using a Respondent Driven Sampling method was conducted across the six regions of country among FSW in 2017. A comprehensive questionnaire was used to explore socio-demographic characteristics, sexual history, HIV knowledge, and sexual behaviors. HIV rapid tests were used to assess HIV infection. Results A total of 1,036 FSW, with a median age of 26 years old [interquartile range (IQR): 22–33], participated in the study, with 49.2% (n = 510) of them having reached secondary school. Median age at first sexual intercourse was 20 years old [IQR: 17–25] and estimated number of clients per week was of 5 [IQR: 3–10]. A total of 936 (95.6%) reported the use of a condom during last sexual intercourse with a client and 493 (47.6%) reported the use of a condom during their last sexual intercourse with a partner or husband. HIV prevalence was 13.2% [95% CI: 11.2 – 15.4], and was associated with age (being between 26 and 32 years old; aOR = 4.5; 95% CI: [2.4 – 9.1], p p = 0.012) and the number of partners per week (more than 2 and 3 partners; aOR = 2.5; 95% CI [1.2—5.2]; p = 0.014). Conclusions HIV prevalence and sexual risk behaviors remain high among FSW in Togo, despite prevention efforts aimed at curbing this trend. Other factors, such as access and availability of condoms, the social and legal environment in which FSW operate, should be considered for HIV prevention strategies in this population.