Earthquake (EQ) prediction is an essential topic in recent geophysics and disaster management. In order to explain EQ precursory phenomena, especially the ionospheric perturbations, a few hypotheses have been proposed as the mechanism of lithosphere‐atmosphere‐ionosphere coupling. The most reliable seems to be the atmospheric gravity wave (AGW) hypothesis, because a lot of subionospheric very low frequency (VLF) observations and also ground surface measurements support this hypothesis. However, no direct signature of AGW activity in the middle atmosphere has been yet obtained. So in this study, we have used the ERA5 reanalysis data to investigate the tempo‐spatial evolution of stratospheric AGW activity before a recent huge seismic event of the 2016 Kumamoto EQ on 15 April (Mw7.2). It was found that the AGW potential energy is enhanced significantly during about 1 week before the EQ. The enhancement was mainly distributed around the EQ epicenter and expanded toward eastern Japan. The AGW activity was highest around 11 April, then it calmed down and returned to the background level right before the EQ. These results were compared with the subionospheric VLF observations during the same period, and then the tempo‐spatial evolutions of the lower ionospheric perturbation are found to be very consistent with the stratospheric behavior. The present paper reports on the first finding that the abnormal AGW activity in the stratosphere is detected before a major EQ, and the coincidence of stratospheric AGW activity with VLF subionospheric perturbations provides further support to the AGW hypothesis of the lithosphere‐atmosphere‐ionosphere coupling process.