There is no reliable estimate of the size of female sex workers (FSWs). This study aimed to estimate the size of FSWs in south of Tehran, Iran in 2016 using direct capture-recapture method. In the capture phase, the hangouts of FSWs were mapped as their meeting places. FSWs who agreed to participate in the study tagged with a T-shirt. The recapture phase was implemented at the same places tagging FSWs with a blue bracelet. The total estimated size of FSWs was 690 (95% CI 633, 747). About 89.43% of FSWs experienced sexual intercourse prior to age 20. The prevalence of human immunodeficiency virus infection among FSWs was 4.60%. The estimated population size of FSWs was much more than our expectation. This issue must be the focus of special attention for planning prevention strategies. However, alternative estimates require to estimating the number FSWs, reliably.