The combination of inadequate health systems and the occurrence of humanitarian crisis results in significant logistics and supply chain management (LSCM) challenges in the support of their vulnerable populations. Because of the high cost of humanitarian LSCM and the limited funding available, it is important that organizations make the most of their limited resources. The aim of this research is to develop our understanding of the drivers of LSCM cost in a humanitarian setting. The paper explores the importance of a range of different underpinning potential factors impacting the cost per beneficiary and develops a resultant set of hypotheses tested with a robust regression model. The results demonstrate that the number of beneficiaries and the type of organization, the country’s gross domestic product (GDP) per capita, and the type of health programme all affect the supply chain costs per beneficiary. This research helps further the understanding of the drivers of efficiency for humanitarian supply chains and the impact of health programme design on supply chain costs.