We examined the thermospheric and ionospheric responses to the solar flare on 28 October 2003, utilizing simultaneous observations of the electron and neutral density from the CHAMP satellite. Rapid thermospheric response within a few minutes was observed. In addition, the neutral and plasma perturbations contrasted each other remarkably. First, their temporal development differed. Though started nearly simultaneously, the plasma perturbation developed much faster and to a larger amplitude than its neutral counterpart. Second, their latitudinal distributions differed. At the initial stage of the response, the neutral density was enhanced by 20% almost homogeneously at all latitudes below 50°N/S. In comparison, the plasma disturbance exhibited a distinctive latitudinal structure, with largest density enhancements of 68% at the dip equator, moderate increase of ∼20% at midlatitudes, and depression up to 35% around 15°N/S. This suggests a decoupling between the neutral and plasma disturbances during this stage. The plasma-neutral coupling via ion drag was found to become important about 2–3 hours after the flare bursts. Another interesting feature is that the equatorial ionization anomaly was significantly weakened during the flare. The observations demonstrated that electrodynamics related to the equatorial fountain dominated the photochemistry in controlling the flare-induced plasma density disturbances on 28 October 2003. This differs considerably from the nearly linear cos(SZA) dependence of flare-induced total electron content enhancements.