Background Limited data exists on the association of war trauma with comorbid posttraumatic stress disorder (PTSD)-depression in the general population of low-income countries. The present study aimed to evaluate socioeconomic and trauma-related risk factors associated with PTSD, depression, and PTSD-depression comorbidity in the population of Greater Bahr el Ghazal States, South Sudan. Methods In this cross-sectional community study (n=1200) we applied the Harvard Trauma Questionnaire (HTQ) and MINI International Neuropsychiatric Interview (MINI) to investigate the prevalence of PTSD, depression, and PTSD-depression comorbidity. Multinomial logistic regression analyses were conducted to examine the association between these disorders, previous trauma exposure, sociodemographic, and socioeconomic factors. Results PTSD only was found in 331 (28%) and depression only in 75 (6.4%) of the study population. One hundred and twelve (9.5%) of the participants had PTSD-depression comorbid diagnosis. Exposure to traumatic events and socioeconomic disadvantage were significantly associated with having PTSD or PTSD-depression comorbidity but not with depression. Participants with a comorbid condition were more likely to be socioeconomic disadvantaged, have experienced more traumatic events, and showed higher level of psychological distress than participants with PTSD or depression alone. Conclusions In individuals exposed to war trauma, attention should be given to those who may fulfill criteria for a diagnosis of both PTSD and depression.