Rock heterogeneity can lead to the variation of capillary pressure within a reservoir, also termed ‘capillary heterogeneity’. Research has found that this capillary heterogeneity can lead to variations in the upscaled relative permeability. In this work, we investigate the upscaled impact of capillary heterogeneity on CO2 plume migration. We build a 3D reservoir model of the Endurance proposed CCS site in the UK. The model incorporates geological information publicly available under the Northern Endurance Partnership project. The upscaling scheme we apply is a novel 3D capillary-limit upscaling scheme using invasion percolation theory. The upscaling scheme produces heterogeneous, upscaled porosity, permeability, capillary pressure and relative permeability within each upscaled grid block. We simulate CO2 injection into this model using ECLIPSE. To investigate the impact of capillary heterogeneity on CO2 plume migration, we generate different reservoir models with different levels of heterogeneity. The first model, called ‘VL Zero’ incorporates a homogeneous, viscous-limit relative permeability and the upscaled capillary pressure within each grid block is set to zero. This represents a model where the impact of capillary heterogeneity is disregarded and not upscaled. The ‘CL Pc’ model represents the fully heterogeneous model, where a heterogeneous, upscaled capillary-limit relative permeability and heterogeneous, upscaled capillary pressure is implemented in each grid. This model represents a model where the impact of capillary heterogeneity is fully accounted for. Comparison of the fluid behaviour in these two reservoir models provides an insight into the flow variations due to capillary heterogeneity. The Eclipse data files provided in this dataset can be used to simulate CO2 injection into the reservoir model.