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Abstract We provide observational evidence that the stability of the stratospheric Polar vortex (PV) is a significant driver of sub‐seasonal variability in the thermosphere during geomagnetically quiet times when the PV is anomalously strong or weak. We find strong positive correlations between the Northern Annular Mode (NAM) index and subseasonal (10–90 days) Global Observations of the Limb and Disk (GOLD) O/N₂perturbations at low to mid‐northern latitudes, with a largest value of +0.55 at ∼30.0°N when anomalously strong or weak (NAM >2.5 or < −2.1) vortex times are considered. Strong agreement for O/N₂variability and O/N₂‐NAM correlations is found between GOLD observations and the Whole Atmosphere Community Climate Model with thermosphere‐ionosphere eXtension (WACCM‐X) simulations, which is then used to delineate the global distribution of O/N₂‐NAM correlations. We find negative correlations between subseasonal variability in WACCM‐X O/N₂and NAM at high northern and southern latitudes (as large as −0.54 at ∼60.0°S during anomalous vortex times). These correlations suggest that PV driven upwelling at low latitudes is accompanied by corresponding downwelling at high latitudes in the lower thermosphere (∼80–120 km), which is confirmed using calculations of residual mean meridional circulation from WACCM‐X.