This paper reports the first comparison between comprehensive observations of equatorward moving traveling ionospheric disturbance at midlatitudes and thermospheric general circulation model with high-latitude energy input based on data assimilation. A prominent traveling ionospheric disturbance (TID) was observed during the major magnetic storm of 31 March 2001. The TID propagated from north to south over Japan with phase speeds of 370–640 m/s. The assimilative mapping of ionospheric electrodynamics (AMIE) technique was used as input to the thermosphere-ionosphere-electrodynamics general circulation model (TIEGCM) to investigate generation and propagation of the observed TID. In the model, two Joule heating enhancements in the high-latitude dayside sector produced two distinct traveling atmospheric waves (TADs), which propagated to Japan in the midnight sector as enhancements in thermospheric temperature and southward wind speed. The phase speed of the TADs was much faster (∼1100 m/s) in the model, probably due to the overestimation of Joule heating in the model. The second TAD corresponds to the observed prominent TID, while signatures of the first TAD were also seen in the observed ionosonde data. The observed TID was characterized by a decrease in southward wind speed, causing a significant F-layer height decrease and a temporal enhancement of F-layer peak density. These characteristics were reproduced by the model as a rarefaction of the second TAD. The temporal enhancement of F-layer peak density was because of the vertical shear of meridional wind. The absolute value of F-layer electron density in the model was several factors smaller than that observed, probably because of the underestimation of the supply of O⁺ ions from the plasmasphere.