In South Sudan, the civil war in 2016 led to mass displacement in Juba that rapidly spread to other regions of the country. Access to health care was limited because of attacks against health facilities and workers and pregnant women and newborns were among the most vulnerable. Translation of newborn guidelines into public health practice, particularly during periods of on-going violence, are not well studied during humanitarian emergencies. During 2016 to 2017, we assessed the delivery of a package of community- and facility-based newborn health interventions in displaced person camps to understand implementation outcomes. This case analysis describes the challenges encountered and mitigating strategies employed during the conduct of an original research study.