Poor adherence to safe water chain practices is a major obstacle to consumption of safe drinking water. In refugee settings, adherence to safe water chain is critical in minimizing water-related diseases. Despite this, little is known about the level of adherence to safe water chain and associated factors, especially in emergency settings. In this study, we interviewed 400 household heads in Pagrinya refugee camp in Northern Uganda and assessed household level adherence to safe water chain practice and associated factors. Modified Poisson regression was used to model the association between adherence to safe water chain and independent variables. All households utilized improved water sources and 74.0% had high adherence to safe water chain. Having post-primary education and high level of knowledge about the safe water chain were positive predictors of high adherence to the safe water chain while round travel time exceeding 1 hour during water collection was negatively associated with high adherence. There is a need for awareness campaigns on safe water chain maintenance among refugees without any formal education. Constructing more water sources would also minimize round travel time during water collection and enable households to collect sufficient water that enables hygienic water storage and use.