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Abstract Paleotemperature reconstructions from ice cores are mixed signals of changes in climate and ice‐surface elevation. A common, temperature‐based paleoaltimetry method suggests these signals can be disentangled by comparing two proxy locations with similar climates. The difference between the records is assumed to be due to elevation, which is estimated by scaling the temperature difference by a lapse rate. We investigate the uncertainty associated with this approach using a case study of the Antarctic Ice Sheet during the Last Glacial Maximum. From an ensemble of climate simulations, we extract modeled temperatures at locations of real ice cores. We find uncertainty on the order of hundreds of meters that results from spatial heterogeneity in non‐adiabatic temperature change, which itself stems in part from elevation‐induced atmospheric circulation change. Our findings suggest that caution is needed when interpreting temperature‐based paleoaltimetry results for ice sheets.