Background Under-five children born in a fragile and war-affected setting of South Sudan are faced with a high risk of death as reflecting in high under-five mortality. In South Sudan health inequities and inequitable condition of daily living play a significant role in childhood mortality. This study examines factors associated with under-five mortality in South Sudan.

Methods The study population includes 8125 singleton, live birth, under-five children born in South Sudan within 5 years prior to the 2010 South Sudan Household Survey. Factors associated with neonatal, infant and under-five deaths were examined using generalised linear latent and mixed models with the logit link and binomial family that adjusted for cluster and survey weights.

Results The multivariate analysis showed that mothers who reported a previous death of a child reported significantly higher risk of neonatal (adjusted OR (AOR)=3.74, 95% confidence interval (CI 2.88 to 4.87), P<0.001), infant (AOR=3.19, 95% CI (2.62 to 3.88), P<0.001) and under-five deaths (AOR=3.07, 95% CI (2.58 to 3.64), P<0.001). Other associated factors included urban dwellers (AOR=1.37, 95% CI (1.01 to 1.87), P=0.045) for neonatal, (AOR=1.35, 95% CI (1.08 to 1.69), P=0.009) for infants and (AOR=1.39, 95% CI (1.13 to 1.71), P=0.002) for under-five death. Unimproved sources of drinking water were significantly associated with neonatal mortality (AOR=1.91, 95% CI (1.11 to 3.31), P=0.02).

Conclusions This study suggested that the condition and circumstances in which the child is born into, and lives with, play a role in under-five mortality, such as higher mortality among children born to teenage mothers. Ensuring equitable healthcare service delivery to all disadvantaged populations of children in both urban and rural areas is essential but remains a challenge, while violence continues in South Sudan.