We discovered a secular change in the travel time of direct S-waves over a 10-year observation period by means of continuous operation of an artificial and stable seismic source, called Accurately Controlled Routinely Operated Signal System (ACROSS), which is deployed in the central part of Japan along the Nankai Trough. We used 13 High Sensitivity Seismograph Network Japan (Hi-net) stations around the ACROSS source to monitor the temporal variation in travel time. Green’s functions were calculated for each station daily from March 29, 2007, through October 30, 2017. Secular advance in the temporal variation in travel time was seen for the whole operation period, in addition to a steplike delay associated with the 2011 Tohoku earthquake. We estimated the rate of secular change and the amount of coseismic step by modeling the transfer function of S-waves with a linear trend and the coseismic step of the 2011 Tohoku earthquake. Distance dependences of the travel time changes can be explained as a combination of common bias and dispersion for each station, for both the secular and coseismic changes. This can be interpreted as a randomly distributed change in seismic velocity over the range of the observation region. An azimuthal dependence exists for both changes and shows larger changes in the NE–SW direction than in the NW–SE direction from the ACROSS source.