<p>A geochemical database for the basement rocks of the Japanese islands has been constructed. These data were previously published in Japanese domestic journals and bulletins not readily accessible to the international community. The database includes 5818 samples from 224 articles, and provides major and trace element concentrations, isotopic ratios, geographical coordinates (latitude, longitude, and altitude) of sampling points, and geological and lithological information. These data are provided in a unified and consistent format as an Excel spreadsheet, which can be efficiently utilized for statistical analyses and data-driven approaches in geochemistry, geology, and petrology.</p>