Female sex workers (FSWs) frequently face violence in their working place. This study assessed the physical and sexual violence and associated factors among FSWs in Rwanda. A cross-sectional study was conducted among FSWs in Rwanda in 2015. Venue-Day-Time sampling method was used for recruitment. Descriptive analyses and logistic regression models were computed to assess factors associated with violence. In total, 1978 FSWs were recruited. A large proportion (18.3%) had been sexually abused outside of the family circle, and 37.8% had faced physical violence before 15 years of age. Clients were most often reported (67.0%) as perpetrators of physical violence in sex work. Being aged 25 years old and above, and having sexually transmitted infections (STIs) were positively associated with sexual violence (aOR = 2.1[95%CI: 1.80-2.39]) and (aOR = 3.0[95%CI: 1.01-2.14], respectively). Being aged 25 years old and above (aOR = 0.8[95%CI: 0.76-0.89]) and drinking alcohol every day (aOR = 0.6[95%CI: 0.42-0.87]) were negatively associated with physical violence. Sexual and physical violence was common among FSWs in Rwanda. Single FSWs are the most vulnerable to sexual violence. Alcohol consumption and having STIs are associated with violence against FSWs. Human rights and social protection as well as health promotion among FSWs is needed.