This study examines how thermospheric motions due to gravity waves (GWs) drive ion upflow in the F region, modulating the topside ionosphere in a way that can contribute to ion outflow. We present incoherent scatter radar data from Sondrestrom, from 31 May 2003 which showed upflow/downflow motions, having a downward phase progression, in the field‐aligned velocity, indicating forcing by a thermospheric GW. The GW‐upflow coupling dynamics are investigated through the use of a coupled atmosphere‐ionosphere model to examine potential impacts on topside ionospheric upflow. Specifically, a sequence of simulations with varying wave amplitude is conducted to determine responses to a range of transient forcing reminiscent of the incoherent scatter radar data. Nonlinear wave effects, resulting from increases in amplitude of the modeled GW, are shown to critically impact the ionospheric response. GW breaking deposits energy into smaller scale wave modes, drives periods of large field‐aligned ion velocities, while also modulating ion densities. Complementary momentum transfer increases the mean flow and, through ion‐neutral drag, can increase ion densities above 300 km. Ionospheric collision frequency (cooling) and photoionization effects (heating), both dependent on ionospheric density, modify the electron temperature; these changes conduct quickly up geomagnetic field lines driving ion upflow at altitudes well above initial disturbances. This flow alters ion populations available for high‐altitude acceleration processes that may lead to outflow into the magnetosphere. We have included a representative source of transverse wave heating which, when supplemented by our GWs, illustrates strengthened upward fluxes in the topside ionosphere.