Monitoring of earthquake faults and volcanoes contributes to our understanding of their dynamic mechanisms and to our ability to predict future earthquakes and volcanic activity. We report here on spatial and temporal variations of seismic velocity around the seismogenic fault of the 2016 Kumamoto earthquake [moment magnitude (Mw) 7.0] based on ambient seismic noise. Seismic velocity near the rupture faults and Aso volcano decreased during the earthquake. The velocity reduction near the faults may have been due to formation damage, a change in stress state, and an increase in pore pressure. Further, we mapped the post-earthquake fault-healing process. The largest seismic velocity reduction observed at Aso volcano during the earthquake was likely caused by pressurized volcanic fluids, and the large increase in seismic velocity at the volcano’s magma body observed ~3 months after the earthquake may have been a response to depressurization caused by the eruption. This study demonstrates the usefulness of continuous monitoring of faults and volcanoes.