The association between poor mental health and factors related to HIV acquisition and disease progression (also referred to as HIV-related factors) may be stronger among conflict-affected populations given elevated rates of mental health disorders. We conducted a scoping review of the literature to identify evidence-based associations between mental health (depression, anxiety, and post-traumatic stress disorder [PTSD]) and factors related to HIV acquisition and progression in conflict-affected populations. Five electronic databases were searched on October 10, 2014 and updated on March 7, 2017 to identify peer-reviewed publications presenting primary data from January 1, 1994 to March 7, 2017. Articles were included if: 1) depression, anxiety, and/or PTSD was assessed using a validated scale, 2) HIV or HIV-related factors were a primary focus, 3) quantitative associations between depression/anxiety/PTSD and HIV or HIV-related factors were assessed, and 4) the study population was conflict-affected and from a conflict-affected setting. Of 714 citations identified, 33 articles covering 110,818 participants were included. Most were from sub-Saharan Africa (n = 25), five were from the USA, and one each was from the Middle East, Europe, and Latin America. There were 23 cross-sectional, 3 time-series, and 7 cohort studies. The search identified that mental health has been quantitatively associated with the following categories of HIV-related factors in conflict-affected populations: markers of HIV risk, HIV-related health status, sexual risk behaviors, and HIV risk exposures (i.e. sexual violence). Further, findings suggest that symptoms of poor mental health are associated with sexual risk behaviors and HIV markers, while HIV risk exposures and health status are associated with symptoms of poor mental health. Results suggest a role for greater integration and referrals across HIV and mental health programs for conflict-affected populations.Electronic supplementary materialThe online version of this article (10.1186/s13031-018-0156-y) contains supplementary material, which is available to authorized users.