BACKGROUND: Over 40% of all deaths among children under 5 are neonatal deaths (0-28 days), and this proportion is increasing. In 2012, 2.9 million newborns died, with 99% occurring in low- and middle-income countries. Many of the countries with the highest neonatal mortality rates globally are currently or have recently been affected by complex humanitarian emergencies. Despite the global burden of neonatal morbidity and mortality and risks inherent in complex emergency situations, research investments are not commensurate to burden and little is known about the epidemiology or best practices for neonatal survival in these settings. METHODS: We used the Child Health and Nutrition Research Initiative (CHNRI) methodology to prioritize research questions on neonatal health in complex humanitarian emergencies. Experts evaluated 35 questions using four criteria (answerability, feasibility, relevance, equity) with three subcomponents per criterion. Using SAS 9.2, a research prioritization score (RPS) and average expert agreement score (AEA) were calculated for each question. RESULTS: Twenty-eight experts evaluated all 35 questions. RPS ranged from 0.846 to 0.679 and the AEA ranged from 0.667 to 0.411. The top ten research priorities covered a range of issues but generally fell into two categories- epidemiologic and programmatic components of neonatal health. The highest ranked question in this survey was "What strategies are effective in increasing demand for, and use of skilled attendance?" CONCLUSIONS: In this study, a diverse group of experts used the CHRNI methodology to systematically identify and determine research priorities for neonatal health and survival in complex humanitarian emergencies. The priorities included the need to better understand the magnitude of the disease burden and interventions to improve neonatal health in complex humanitarian emergencies. The findings from this study will provide guidance to researchers and program implementers in neonatal and complex humanitarian fields to engage on the research priorities needed to save lives most at risk.