To assess the effects of sexual violence (SV) in armed conflicts on women’s mental health, on its own and in conjunction with reproductive health issues such as fistula or chronic pelvic pain (CPP). A cross-sectional population-based study of 320 women living in Goma, the Democratic Republic of Congo, aged 15 to 45 years, was conducted. Women who experienced conflict-related sexual violence (CRSV) were compared with those who experienced non-conflict-related sexual violence (NCRSV) and those who never experienced such acts. Data were gathered through individual interviews by local staff using standardized questionnaires. The outcomes investigated were post-traumatic stress disorder (PTSD) symptoms severity and psychological distress symptoms (PDS) severity. Experience of SV in either context was associated with more severe PDS (p < .0001). Only CRSV was associated with more severe PTSD symptoms (p < .0001). Women who suffered from fistula or CPP also had a higher PDS score mean (p < .0001 and p = .007) and a higher PTSD symptoms score mean (p < .0001, for both reproductive health issues). Multivariate analyses showed that compared with women who never experienced SV and never suffered from fistula or CPP, those who experienced CRSV and suffered from fistula or CPP had the most severe PDS and PTSD symptoms after adjustment for potential confounders. The differences in PDS and PTSD symptoms severity were all significant (p < .0001). Psychological and physical health care are urgently needed for women who experienced CRSV, particularly those with additional issues of fistula or CPP. Current interventions should simultaneously seek to improve both reproductive and mental health.