Background Despite Burundi having formed a network of 112 health facilities that provide emergency obstetric and neonatal care (EmONC), the country continues to struggle with high rates of maternal and newborn deaths. There is a dearth of empirical evidence on the capacity and performance of EmONC health facilities and on the real needs to inform proper planning and policy. Our study aims to generate evidence on the capacity and performance of EmONC health facilities in Burundi and examine how the country might develop an appropriate skilled delivery care workforce to improve maternal and newborn survival. Methods We will use a sequential design where each study phase serially inputs into the subsequent phase. Three main study phases will be carried out: i) an initial policy document review to explore global norms and local policy intentions for EmONC staffing and ii) a cross-sectional survey of all EmONC health facilities to determine what percent of facilities are functional including geographic and population coverage gaps, identify staffing gaps assessed against norms, and identify other needs for health facility strengthening. Finally, we will conduct surveys in schools and different ministries to examine training and staffing costs to inform staffing options that might best promote service delivery with adequate budget impacts to increase efficiency. Throughout the study, we will engage stakeholders to provide input into what is reasonable staffing norms as well as feasible staffing alternatives within Burundi’s budget capacity. Analytical models will be used to develop staffing proposals over a realistic policy timeline. Conclusion Evidence-based health planning improves cost-effectiveness and reduces wastage within scarce and resource-constrained contexts. This study will be the first large-scale research in Burundi that builds on stakeholder support to generate evidence on the capacity of designated EmONC health facilities including human resources diagnosis and develop staffing skill-mix tradeoffs for policy discussion.