The effects of breaking of traveling, planetary scale Rossby waves (TPWs) in the lower thermosphere are investigated with respect to the mixing of neutral constituents. We use numerical simulations of the Whole Atmosphere Community Climate Model, eXtended version, whose meteorology below 92 km is constrained by atmospheric specifications obtained from operational weather forecast/data assimilation system. The Fourier spectra show that the amplitude of TPWs with periods between 3 and 10 days are statistically significant in some years; the amplitude and phase of the band‐pass filtered behavior is consistent with the behavior of the 5 day wave. A wavelet analysis using the S‐transform shows that large variations with periods between 3 and 10 days can occur in relatively narrow temporal windows (20–30 days) during boreal winter. The momentum flux entering the lower thermosphere during the times of TPW amplification is shown to be large, and the amplifications of the TPWs in the thermosphere are not always associated with stratospheric sudden warming. The subtropical zonal accelerations are consistent with Rossby wave encountering a surf zone at low latitudes, resulting in wave breaking. The zonal acceleration is shown to be associated with a meridional diffusion, which is largest in the lower thermosphere where the wave activity and the wave breaking are also large. The ultimate effect on neutral density and composition is a meridional, down‐gradient mixing; although this horizontal diffusion is largest below 110 km, the effects on the composition are amplified with increasing altitude, due to the diffusive separation of the thermosphere.