Objective To assess gender-based violence and mental health outcomes among a population of female urban refugees and asylum seekers. Methods In a questionnaire-based, cross-sectional study conducted in 2010 in Kampala, Uganda, a study team interviewed a stratified random sample of female refugees and asylum seekers aged 15–59 years from the Democratic Republic of Congo and Somalia. Questionnaires were used to collect information about recent and lifetime exposure to sexual and physical violence, and symptoms of depression and post-traumatic stress disorder (PTSD). Results Among the 500 women selected, 117 (23.4%) completed interviews. The weighted lifetime prevalences of experiencing any (physical and/or sexual) violence, physical violence, and sexual violence were 77.5% (95% CI 66.6–88.4), 76.2% (95% CI 65.2–87.2), and 63.3% (95% CI 51.2–75.4), respectively. Lifetime history of physical violence was associated with PTSD symptoms ( P P = 0.014). Overall, 112 women had symptoms of depression (weighted prevalence 92.0; 95% CI 83.9–100) and 83 had PTSD symptoms (weighted prevalence 71.1; 95% CI 59.9–82.4). Conclusion Prevalences of violence, depression, and PTSD symptoms among female urban refugees in Kampala are high. Additional services and increased availability of psychosocial programs for refugees are needed.