This paper presents a comprehensive modeling investigation of ionospheric and thermospheric variations during a prompt penetration electric field (PPEF) event that took place on 9 November 2004, using the Thermosphere‐Ionosphere‐Mesosphere Electrodynamic General Circulation Model (TIMEGCM). The simulation results reveal complex latitudinal and longitudinal/local‐time variations in vertical ion drift in the middle‐ and low‐latitude regions owing to the competing influences of electric fields and neutral winds. It is found that electric fields are the dominant driver of vertical ion drift at the magnetic equator; at midlatitudes, however, vertical ion drift driven by disturbance meridional winds exceeds that driven by electric fields. The temporal evolution of the UT‐latitude electron density profile from the simulation depicts clearly a super‐fountain effect caused by the PPEF, including the initial slow‐rise of the equatorial F‐layer peak height, the split of the F‐layer peak density, and the subsequent downward diffusion of the density peaks along magnetic field lines. Correspondingly, low‐latitude total electron content (TEC) becomes bifurcated around the magnetic equator. The O/N2column density ratio, on the other hand, shows very little variations during this PPEF event, excluding composition change as a potential mechanism for the TEC variations. By using realistic, time‐dependent, high‐latitude electric potential and auroral precipitation patterns to drive the TIMEGCM, the model is able to successfully reproduce the large vertical ion drift of ∼120 m/s over the Jicamarca incoherent radar (IS) in Peru, which is the largest daytime ion drift ever recorded by the radar. The simulation results are validated with several key observations from IS radars, ground GPS‐TEC network, and the TIMED‐GUVI O/N2column density ratio. The model‐data intercomparison also reveals some deficiencies in the TIMEGCM, particularly the limitations imposed by its upper boundary height as well as the prescribed O+ flux.
