The ability to perform data assimilation in the Whole Atmosphere Community Climate Model eXtended version (WACCMX) is implemented using the Data Assimilation Research Testbed (DART) ensemble adjustment Kalman filter. Results are presented demonstrating that WACCMX+DART analysis fields reproduce the middle and upper atmosphere variability during the 2009 major sudden stratospheric warming (SSW) event. Compared to specified dynamics WACCMX, which constrains the meteorology by nudging toward an external reanalysis, the large‐scale dynamical variability of the stratosphere, mesosphere, and lower thermosphere is improved in WACCMX+DART. This leads to WACCMX+DART better representing the downward transport of chemical species from the mesosphere into the stratosphere following the SSW. WACCMX+DART also reproduces most aspects of the observed variability in ionosphere total electron content and equatorial vertical plasma drift during the SSW. Hindcast experiments initialized on 5, 10, 15, 20, and 25 January are used to assess the middle and upper atmosphere predictability in WACCMX+DART. A SSW, along with the associated middle and upper atmosphere variability, is initially predicted in the hindcast initialized on 15 January, which is ∼10 days prior to the warming. However, it is not until the hindcast initialized on 20 January that a major SSW is forecast to occur. The hindcast experiments reveal that dominant features of the total electron content can be forecasted ∼10–20 days in advance. This demonstrates that whole atmosphere models that properly account for variability in lower atmosphere forcing can potentially extend the ionosphere‐thermosphere forecast range.