Fluid-inclusion and thermochronometric analyses have been applied to hydrothermal alteration zones and their host rocks outcropping in the Hongu area of the Kii Peninsula, southwestern Japan in an attempt to detect thermal anomalies related to hydrothermal events and quantify the thermal effects on the host rocks. Hydrothermal events at ~150°C and ~200°C were identified by fluid-inclusion microthermometry of quartz veins in the alteration zones. For the host rocks and alteration zones, in the youngest population zircon yielded U–Pb dates ranging between ~74.7–59.2 Ma, fission-track dates of ~27.2–16.6 Ma, and (U–Th)/He single-grain dates of ~23.6–8.7 Ma. Apatite yielded pooled fission-track ages of ~14.9–9.0 Ma. The zircon U–Pb dates constrain the maximum depositional ages of the sedimentary samples. However, the fission-track and (U–Th)/He dates show no clear trend as a function of distance from the alteration zones. Hence, no thermal anomaly was detected in the surrounding host rocks based on the thermochronometric data patterns. The fission-track and (U–Th)/He dates are rather thought to record regional thermal and exhumation histories rather than a direct thermal imprint of fluid flow, probably because the duration of such activity was too short or because fluid flow occurred before regional cooling events and were later thermally overprinted. Apatite fission-track ages of ~10 Ma may reflect regional mountain uplift and exhumation related to the obduction of the SW Japan lithospheric sliver onto the Shikoku Basin, or the rapid subduction of the Philippine Sea slab associated with the clockwise rotation of the Southwest Japan Arc.