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Abstract Background Approximately 2.7 million neonatal deaths occur annually, with highest rates of neonatal mortality in countries that have recently experienced conflict. Constant instability in South Sudan further strains a weakened health system and poses public health challenges during the neonatal period. We aimed to describe the state of newborn facility-level care in displaced person camps across Juba, Malakal, and Maban. Methods We conducted clinical observations of the labor and delivery period, exit interviews with recently delivered mothers, health facility assessments, and direct observations of midwife time-use. Study participants were mother-newborn pairs who sought services and birth attendants who provided delivery services between April and June 2016 in five health facilities. Results Facilities were found to be lacking the recommended medical supplies for essential newborn care. Two of the five facilities had skilled midwives working during all operating hours, with 6.2% of their time spent on postnatal care. Selected components of thermal care (62.5%), infection prevention (74.8%), and feeding support (63.6%) were commonly practiced, but postnatal monitoring (27.7%) was less consistently observed. Differences were found when comparing the primary care level to the hospital (thermal: relative risk [RR] 0.48 [95% CI] 0.40–0.58; infection: RR 1.28 [1.11–1.47]; feeding: RR 0.49 [0.40–0.58]; postnatal: RR 3.17 [2.01–5.00]). In the primary care level, relative to newborns delivered by traditional birth attendants, those delivered by skilled attendants were more likely to receive postnatal monitoring (RR 1.59 [1.09-2.32]), but other practices were not statistically different. Mothers’ knowledge of danger signs was poor, with fever as the highest reported (44.8%) followed by not feeding well (41.0%), difficulty breathing (28.9%), reduced activity (27.7%), feeling cold (18.0%) and convulsions (11.2%). Conclusions Addressing health service delivery in contexts affected by conflict is vital to reducing the global newborn mortality rate and reaching the Sustainable Development Goals. Gaps in intrapartum and postnatal care, particularly skilled care at birth, suggest a critical need to build the capacity of the existing health workforce while increasing access to skilled deliveries.