Conducting flood susceptibility assessments is critical for the identification of flood hazard zones and the mitigation of the detrimental impacts of floods in the future through improved flood management measures. The significance of this study is that we create ensemble methods using the per-pixel approaches of frequency ratio (FR), analytical hierarchical process (AHP), and evidence belief function (EBF) used for weightings with the object-based ‘geons’ approach used for aggregation to create a flood susceptibility map for the East Rapti Basin in Nepal. We selected eight flood conditioning factors considered to be relevant in the study area. The flood inventory data for the East Rapti basin was derived from past flood inventory datasets held in the regional database system by the International Centre for Integrated Mountain Development (ICIMOD). The flood inventory was classified into training and validation datasets based on the widely used split ratio of 70/30. The Receiver Operating Characteristic (ROC) was used to determine the accuracy of the flood susceptibility maps. The AUC results indicated that the combined per-pixel and object-based geon approaches yielded better results than the per-pixel approaches alone. Our results showed that the object-based geon approach creates meaningful regional units that are beneficial for future planning.