During a large geomagnetic storm, the electric field from the polar ionosphere can expand far enough to affect the mid-latitude and equatorial electric fields. These changes in the equatorial zonal electric field, called the penetration field, will cause changes in the meridional ion flows that can be observed by radars and spacecraft. In general this <b><i>E</i></b> &times; <b><i>B</i></b> ion flow near the equator caused by the penetration field during undershielding conditions will be upward on the dayside and downward on the nightside of the Earth. Previous analysis of the equatorial meridional flows observed by CINDI instrument on the C/NOFS spacecraft during the 26 September 2011 storm showed that all of the response flows on the dayside were excess downward flows instead of the expected upward flows. These observed storm-time responses are compared to a prediction from a physics-based coupled model of thermosphere–ionosphere–inner-magnetosphere in an effort to explain these observations. The model results suggest that the equatorial downward flow could be attributed to a combined effect of the overshielding and disturbance dynamo processes. However, some discrepancy between the model and observation indicates a need for improving our understanding of how sensitive the equatorial electric field is to various model input parameters that describe the magnetosphere–ionosphere coupling processes.