Dome Fuji, inland East Antarctica is one of only few regions where 1.5-Ma old ice can be preserved for investigating the mid-Pleistocene Transition. We used stochastic simulation and various radar datasets to generate a bed topography ensemble with the continuous, realistic roughness necessary to assess basal conditions. Ensemble analysis reveals the magnitude and spatial distribution of topographic uncertainty, facilitating uncertainty-constrained assessments of subglacial drainage and topographic adjustments to geothermal heat flow. We find that topographic variability can lead to widespread local geothermal heat flow variations of ± 20% the background value, which aggregate to raise the regional value and suggest previously underestimated distributions and rates of basal melting. We also find that survey profile spacing has an increasing influence on topographic uncertainty for rougher bed, deriving an empirical relationship that could guide future survey planning based on uncertainty tolerance.