In order to elucidate the process of mineralization of clay minerals in fault gouge and its spatial-temporal relationship with fault-zone evolution and hydrothermal alteration, X-ray diffraction (XRD) analysis and K-Ar dating were performed on clay samples from the Kojaku Granite of central Japan, including fault gouge along an active fault. The area studied is suitable for understanding thermal constraints on clay mineralization because the wall rock is homogeneous and its thermal history well defined. The results from XRD indicated that the clay minerals in the gouge samples are dioctahedral smectite, kaolinite, and 1Md illite, whereas clay fillings in fractures and joints in the intact granite (clay vein) include 2M1 illite in addition to dioctahedral smectite and 1Md illite. The evolution of clay mineralization is reconstructed as follows: (1) high-temperature hydrothermal alteration of feldspar and biotite produced 2M1 illite in clay veins; and (2) alteration accompanied by shearing at a lower temperature resulted in the formation of 1Md illite in the gouges. This scenario is consistent with the cooling history of the granite constrained by fission-track, U-Pb, and K-Ar dating methods. K-Ar dating of the clay samples separated into multiple particle-size fractions indicated that the low-temperature alteration leading to the production of 1Md illite was dated to ~40 Ma. Based on the cooling history of the granite, the 1Md illite formed at temperatures of 60–120°C. This temperature range was at the lower limit of the range reported in previous studies for faults. The spatial and geometrical relation of the faults studied and their K-Ar ages infer evolution which can be described as extensive development of small-scale faults at ~40 Ma followed by coalescence of the small-scale faults to form a larger, recently reactivated, active fault. The K-Ar ages have not been reset by the recent near-surface fault activity.