Objectives South Sudan has the lowest percentage of births attended by skilled health personnel in the world. This paper aims to identify potential risk factors associated with non-use of skilled birth attendants at delivery in South Sudan. Methods Secondary data analyses of the 2010 South Sudan Household Health Survey second round were conducted with data for 3504 women aged 15–49 years who gave birth in the 2 years prior to the survey. The risk of non-use of skilled birth attendants was examined using simple and multiple logistic regression analyses. Results The prevalence rates for skilled, unskilled and no birth attendants at delivery were 41 [95 % confidence interval (CI) 38.2, 43.0], 36 [95 % CI 33.9, 38.8], and 23 % [95 % CI 20.6, 24.9] respectively. Multivariable analyses indicated that educated mothers [adjusted odds ratio (AOR) 0.70; 95 % CI 0.57, 0.86], mothers who had three and more complications during pregnancy [AOR 0.77; 95 % CI 0.65, 0.90], mothers who had at least 1–3 ANC visits [AOR 0.38; 95 % CI 0.30, 0.49] and mothers from rich households [AOR 0.52; 95 % CI 0.42, 0.65] were significantly more likely to use skilled birth attendants (SBAs) at delivery. Mothers who lived in rural areas [AOR 1.44; 95 % CI 1.06, 1.96] were less likely to deliver with SBAs. Conclusion Intensive investments to recruit and train more skilled birth attendants’ on appropriate delivery care are needed, as well as building a community-based skilled birth attendants’ program to reduce avoidable maternal mortality in South Sudan.