We have performed simulations using the Naval Research Laboratory's physics‐based model of the ionosphere, Sami3 is A Model of the Ionosphere (SAMI3), to illustrate how neutral wind dynamics is responsible for day‐to‐day variability of the ionosphere. We have used neutral winds specified from the extended version of the specified dynamics Whole Atmosphere Community Climate Model (SD‐WACCM‐X), in which meteorology below 92 km is constrained by atmospheric specifications from an operational weather forecast model and reanalysis. To assess the realism of the simulations against observations, we have carried out a case study during January–February 2009, a dynamically disturbed time characterized by a sudden stratospheric warming (SSW) commencing 24 January 2009. Model results are compared with total electron content (TEC) from Jet Propulsion Laboratory global ionospheric maps....