We processed Global Navigation Satellite System (GNSS) time‐series data to extract total electron content (TEC) perturbations of the ionosphere caused by the Kaikōura earthquake. We used ray‐based modeling to infer which part of the Earth’s surface coupled significant energy from the solid Earth into the atmosphere. We compared modeled TEC data with the observed time‐series data and determined that significant coupling occurred north‐northeast of the initial slip. This work corroborates existing analysis made with geodetic and Interferometric Synthetic Aperture Radar (InSAR) data. The TEC data suggested that the initial rupture coupled some energy into the atmosphere, but later surface displacements ( after the initiation) caused more significant ionospheric perturbations. Using an array of GNSS stations, we were able to track the moveout of the acoustic wave through the ionosphere. We used a method commonly used in seismological studies called backprojection to estimate the location of the source of the TEC perturbation on Earth’s surface. This is the first time that this method has been applied to TEC data, and the results are promising. The backprojection results are slightly shifted in space from the known area of maximum uplift, and we attribute this small discrepancy to the fact that we did not account for horizontal winds in the atmosphere, nor the 3D heterogeneity of the real atmosphere in the travel‐time modeling.