Antarctic ice cores are a unique invaluable archive of past climatic changes over the Antarctic ice sheet. However, as reconstructions are based on the history of surface climate at the ice core site, variations of the surface geometry and the ice flow patterns might result in biases within those reconstructions. In this study, we use results from three transient ice sheet model simulations covering the last two million years to investigate surface height and ice divide variability for major Antarctic ice core sites and ongoing prospective future drilling locations. We find that East Antarctic ice-core site elevations varied by up to 240 m over the glacial cycles of the last 800 kyr, whereas glacial–interglacial surface elevation variability is substantially smaller during earlier periods relevant to prospective oldest ice sites. Simulations using different ice sheet models and climate-forcing approaches produce substantially different long-term surface elevation trends. We further investigate the synchronicity between Antarctic climatic change and simulated surface height variability and find a substantial shift between the timing of maximum interglacial temperature and ice surface elevation. Further, we quantify the variability of the ice divide and ice dome position throughout the time period of the individual ice cores and up to 2 Ma before present for prospective oldest ice cores which varies by up to 120 km. Our study suggests that uncertainty, in ice surface height has to be taken into account when investigating ice core-based Antarctic temperature reconstructions. Further, the results presented in this study serve as initial constraints for further simplified (e.g. 1D) and higher resolution regional simulations of Antarctic ice sheet dynamics at ice core locations.