Seismic velocity measurements have revealed that the Tohoku-Oki earthquake affected velocity structures of volcanic zones far from the epicenter. Using a seismological method based on ambient seismic noise interferometry, we monitored the anisotropy in the Mount Fuji area during the year 2011, in which the Tohoku-Oki earthquake occurred (Mw = 9.0). Here we show that even at 400 km from the epicenter, temporal variations of seismic anisotropy were observed. These variations can be explained by changes in the alignment of cracks or fluid inclusions beneath the volcanic area due to stress perturbations and the propagation of a hydrothermal fluid surge beneath the Hakone hydrothermal volcanic area. Our results demonstrate how a better understanding of the origin of anisotropy and its temporal changes beneath volcanoes and in the crust can provide insight into active processes, and can be used as part of a suite of volcanic monitoring and forecasting tools.