Background To assess whether Healing in Harmony (HiH), a form of music therapy, improved women's mental health following conflict-related trauma and sexual violence in the Democratic Republic of Congo. Methods This study used a step-wedged design and included 167 women, who completed up to two pre-tests, a post-test, and up to two follow-up interviews at 3 and 6 months after completing the program. The Hopkins Symptoms Checklist was used to measure anxiety and depression. The Harvard Trauma Questionnaire was used to measure post-traumatic stress disorder (PTSD). Generalized estimating equations with unstructured covariance were used to estimate mean change in mental health scores and relative risks (RRs) for screening positive. Results Prior to starting the HiH program, 73.9, 84.2, and 68.5% screened positive with median scores being 2.20, 2.70, and 2.06 for depression, anxiety, and PTSD, respectively. The RR for screening positive declined significantly (RR = 0.49 for depression, 0.61 for anxiety, and 0.54 for PTSD) and mean scores declined significantly by −0.54, −0.67, and −0.53 points, respectively, from the pre- to the post-test, declines that were sustained at the 3-month and 6-month follow-up interviews. Conclusion The HiH program was associated with significant improvement in women's mental health that was sustained up to 6 months post completion of the program despite instability in the region and evidence of continued experience of conflict-related trauma during the study. These data support the value of providing psychological care in the context of ongoing humanitarian crises.