Uganda hosts the largest refugee population in Africa and uses a whole-of-society (WoS) approach to refugee protection. This means that diverse state agencies and humanitarian aid organisations provide complementary humanitarian services and assistance within their respective mandates with the common goal of providing holistic refugee protection services. Within this model, refugees seeking humanitarian assistance are assessed and classified according to UNHCR’s universal vulnerability categories, and depending on the vulnerability criteria, their eligibility for humanitarian intervention is determined. This chapter argues that although the humanitarian system was designed to address the needs of the most vulnerable refugees holistically, implementation of programs using the WoS approach is fragmented in practice, and results in unintended effects that enhance existing vulnerabilities or produces new ones. The chapter relies on ethnographic data to provide empirically grounded explanations for the factors that impede the attainment of protection goals through an examination of the structure of humanitarian governance. It highlights the protection gaps that result the structure’s weaknesses and what this means for refugee protection.