AbstractThe mesosphere and lower thermosphere (MLT) plays a critical role in linking the middle and upper atmosphere. However, many General Circulation Models do not model the MLT and those that do remain poorly constrained. We use long‐term meteor radar observations (2005–2021) from Rothera (67°S, 68°W) on the Antarctic Peninsula to evaluate the Whole Atmosphere Community Climate Model with thermosphere‐ionosphere eXtension (WACCM‐X) and investigate interannual variability. We find some significant differences between WACCM‐X and observations. In particular, at upper heights, observations reveal eastwards wintertime (April–September) winds, whereas the model predicts westwards winds. In summer (October–March), the observed winds are northwards but predictions are southwards. Both the model and observations reveal significant interannual variability. We characterize the trend and the correlation between the winds and key phenomena: (a) the 11‐year solar cycle, (b) El Niño Southern Oscillation, (c) Quasi‐Biennial Oscillation and (d) Southern Annular Mode using a linear regression method. Observations of the zonal wind show significant changes with time. The summertime westwards wind near 80 km is weakening by up to 4–5 ms⁻¹ per decade, whilst the eastward wintertime winds around 85–95 km are strengthening at by around 7 ms⁻¹ per decade. We find that at some times of year there are significant correlations between the phenomena and the observed/modeled winds. The significance of this work lies in quantifying the biases in a leading General Circulation Model and demonstrating notable interannual variability in both modeled and observed winds.