ObjectivesThis study examines health facility utilization for pregnancy and delivery care and the health system challenges, in the light of renewed conflict in 2016, in Torit County, South Sudan. We collected monthly facility data retrospectively on total Antenatal Care (ANC) visits, institutional deliveries, major obstetric, and neonatal complications treated from January 2015 to December 2016. We compared 2015 data with that of 2016 when conflict re-started. We also conducted a descriptive qualitative study based on key informant interviews and Focus Group Discussions (FGDs) to explore the health system challenges. We used a thematic approach to analyse qualitative data. Results ANC visits declined by 21% between 2015 and 2016. The proportion of expected births that occurred in facilities declined from 23.6% in 2015 to 16.7% in 2016 (p< 0.001) while the proportion of obstetric complications treated in facilities declined from 58.9% in 2015 to 43.9% in 2016 (p<0.001). The low national budget to fund the health system, evacuation of international health staff, flight of local health workers and disruption of drugs and medical supplies are the health system challenges identified. Economic barriers and perceived poor quality of care were the two main obstacles to access of health care services.