The evolution of the Antarctic ice sheet during the mid-Pliocene warm period (MPWP) remains uncertain and has important implications for our understanding of ice sheet response to modern global warming. The extent to which marine-based sectors of the East Antarctic Ice Sheet (EAIS) retreated during the MPWP is particularly contentious, with geological observations and geochemical analyses being cited to argue for either a relatively minor or a significant ice sheet retreat in response to mid-Pliocene warming. The stability of marine-based ice sheets is intimately linked to bedrock elevation at their grounding lines, and previous ice sheet modeling assumed that Antarctic bedrock elevation during the MPWP was the same as today with the exception of a correction for the crustal response to ice loading. However, various processes may have perturbed bedrock elevation over the past 3 m.y., most notably vertical deflections of the crust driven by mantle convective flow, or dynamic topography. Here we present simulations of mantle convective flow that are consistent with a wide range of present-day observables and use them to predict changes in dynamic topography and reconstruct bedrock elevations during the MPWP. We incorporate these elevations into a simulation of the Antarctic ice sheet during the MPWP and find that the correction for dynamic topography change has a significant effect on the stability of the EAIS within the marine-based Wilkes Basin, with the ice margin in that sector retreating considerably further inland (200–560 km) relative to simulations that do not include this correction for bedrock elevation.