Background There is a general lack of knowledge regarding disability and especially factors that are associated with disability in low-income countries. We aimed to study the overall and gender-specific prevalence of disability, and the association between exposure to traumatic events and disability in a post-conflict setting. Methods We conducted a cross-sectional community based study of four Greater Bahr el Ghazal States, South Sudan (n = 1200). The Harvard Trauma Questionnaire (HTQ) was applied to investigate exposure to trauma events. Disability was measured using the Washington Group Short Measurement Set on Disability, which is an activity-based scale derived from the WHO’s International Classification of Disability, Functioning and Health. Results The estimated prevalence of disability (with severe difficulty) was 3.6% and 13.4% for disability with moderate difficulties. No gender differences were found in disability prevalence. Almost all participants reported exposure to at least one war-related traumatic event. The result of a hierarchical regression analysis showed that, for both men and women, exposure to traumatic events, older age and living in a polygamous marriage increased the likelihood of having a disability. Conclusions The finding of association between traumatic experience and disability underlines the precariousness of the human rights situation for individuals with disability in low-income countries. It also has possible implications for the construction of disability services and for the provision of health services to individuals exposed to traumatic events.