This case study is part of an evaluation of UNESCO’s role in education in emergencies and protracted crises. It aims to analyze UNESCO’s strategic positioning and its participation in system-wide humanitarian response in South Sudan’s education sector. More specifically, it focuses on exploring the significance of the process used to develop the country’s Education Sector Analysis and Plan and the role and contribution of UNESCO’s International Institute for Educational Planning (UNESCO IIEP) therein. The Institute has been supporting South Sudan’s Ministry of Education, Science and Technology since 2012 and, more recently, has supported the Ministry in developing an Education Sector Plan for 2017-2021. The process has developed government capacities at the federal and state levels and built national ownership of the Education Sector Analysis and Plan through a collaborative hands-on approach. Challenges along the way include ensuring the meaningful participation of ministry staff as well as that of humanitarian/development partners, managing divergent stakeholder expectations and, dealing with the ongoing political and economic stability in the country. Overall, the work by UNESCO-IIEP is seen by many partners as a major contribution to the development of South Sudan’s education sector.