We observe ionospheric perturbations caused by the Tohoku earthquake and tsunami of March 11, 2011. Perturbations near the epicenter were found in measurements of ionospheric total electron content (TEC) from 1198 GPS receivers in the Japanese GEONET network. For the first time for this event, we compare these observations with the estimated magnitude and speed of a tsunami-driven atmospheric gravity wave, using an atmosphere-ionosphere-coupling model and a tsunami model of sea-surface height, respectively. Traveling ionospheric disturbances (TIDs) were observed moving away from the epicenter at approximate speeds of 3400 m/s, 1000 m/s and 200–300 m/s, consistent with Rayleigh waves, acoustic waves, and gravity waves, respectively. We focus our analysis on gravity waves moving south and east of the epicenter, since tsunamis propagating in the deep ocean have been shown to produce gravity waves detectable in ionospheric TEC in the past. Observed southeastward gravity wave perturbations, seen 60 min after the earthquake, are mostly between 0.5 to 1.5 TECU, representing up to 5% of the background vertical TEC (VTEC). Comparisons of observed TID gravity waves with the modeled tsunami speed in the ocean and the predicted VTEC perturbation amplitudes from an atmosphere-ionosphere-coupling model show the measurements and models to be in close agreement. Due to the dense GPS network and high earthquake magnitude, these are the clearest observations to date of the effect of a major earthquake and tsunami on the ionosphere near the epicenter. Such observations from a future real-time GPS receiver network could be used to validate tsunami models, confirm the existence of a tsunami, or track its motion where in situ buoy data is not available.