In some cases, water–rock interactions in fault zones can affect radionuclide migration. Here, we analyzed the chemical compositions of well-exposed fault rocks from the strike-slip Atera Fault, Central Japan, in order to understand the variability and behavior of major and selected trace elements. The fault zone has a 1.2-m-wide, smectite-rich fault core and paired damage zones that developed within welded tuff on one side of the core and within granite on the other side. The 30-cm-wide, kaolinite-rich fault gouge is developed in granite cataclasite, and it shows indications of the latest fault activity, while the 1.2-m-wide fault core appears to be older. Hydrogen and oxygen isotope ratios in the clay-rich fault gouges, and carbon and oxygen isotope ratios in carbonates indicate that the two major clay-rich zones formed in bedrock near the surface, consistent with observed deformation structures. Based on chemical analyses, we identified (1) a slight depletion in SiO2, Na2O, K2O, and light rare earth elements at the edges of the 1.2-m-wide fault core, (2) a clear depletion in SiO2, Na2O, K2O, and all rare earth elements except Eu in the 30-cm-wide fault gouge, and (3) an increase in CaO, MnO, and heavy rare earth elements across the entire 1.2-m-wide fault core. Findings (1) and (2) reflect water–rock interactions in the 1.2-m-wide fault core and in the 30-cm-wide fault gouge that resulted in the formation of smectite and kaolinite. Finding (3) reflects carbonate precipitation caused by the addition of basalt fragments from a nearby site to the 1.2-m-wide fault core during faulting, and subsequent sorption reactions of heavy rare earth elements via processes such as complexation with the carbonates.