In the Southern Fossa Magna region in Japan, weak copper mineralization associated with the Pliocene (ca. 4 Ma) Kogarasu granodiorite is newly identified. In contrast to typical granitic rocks in Japan, the plagioclase in this granodiorite is exhibits excess Al suggesting metal fertility for ore mineralization. The hydrothermal alteration halo overprints both the Kogarasu granodiorite and the Miocene (ca. 13 Ma) Okusenjou-dake granodiorite. The alteration exhibits distinct concentric zoning, divided into three zones: a central potassic (potassium feldspar + magnetite) zone, a surrounding advanced-argillic alteration zone, and a peripheral chlorite zone. The advanced-argillic alteration zone hosts breccia pipe and silicified lithocaps, and the latter of which contain ore-grade enargite mineralization. The potassic zone is associated with minor disseminated chalcopyrite. The sericite K-Ar ages from the advanced argillic alteration zone are 5.41 ± 0.14 Ma and 4.28 ± 0.11 Ma, indicating that the hydrothermal system was genetically linked to the emplacement of the Kogarasu granodiorite. The trace element composition of hydrothermal magnetite in the potassic zone is consistent with the features of porphyry copper deposits (PCDs). These spatial alteration patterns and the presence of mineralized lithocaps indicate that this alteration corresponds to a PCD-type mineralization.