Ice cores and other paleotemperature proxies, together with general circulation models, have provided information on past surface temperatures and the atmosphere's composition in different climates. Little is known, however, about past temperatures at high altitudes, which play a crucial role in Earth's radiative energy budget. Paleoclimate records at high-altitude sites are sparse, and the few that are available show poor agreement with climate model predictions. These disagreements could be due to insufficient spatial coverage, spatiotemporal biases, or model physics; new records that can mitigate or avoid these uncertainties are needed. Here, we constrain the change in upper-tropospheric temperature at the global scale during the Last Glacial Maximum (LGM) using the clumped-isotope composition of molecular oxygen trapped in polar ice cores. Aided by global three-dimensional chemical transport modeling, we exploit the intrinsic temperature sensitivity of the clumped-isotope composition of atmospheric oxygen to infer that the upper troposphere (effective mean altitude 10–11 km) was 6–9°C cooler during the LGM than during the late preindustrial Holocene. A complementary energy balance approach supports a minor or negligible steepening of atmospheric lapse rates during the LGM, which is consistent with a range of climate model simulations. Proxy-model disagreements with other high-altitude records may stem from inaccuracies in regional hydroclimate simulation, possibly related to land-atmosphere feedbacks.