Walnuts are rich sources of lipids and polyunsaturated fatty acids and are expected to promote health. There are two Japanese native walnut species: Oni walnut (Juglans ailanthifolia Carr.) and Hime walnut (Juglans subcordiformis Dode.). However, despite the fact that these Japanese native walnuts have long been consumed in local cuisine, their nutritional composition is largely unknown. This study aimed to assess the concentrations of total lipids, and fatty acid composition including polyunsaturated fatty acids, in the kernels of Oni walnut and Hime walnut. In addition, we assessed various aspects related to their nutritional and functional values, by measuring the total protein, amino acids, minerals, and total polyphenols. The concentrations of the measured compounds in the two native species were compared with those in the English walnut (Juglans regia L.), a globally recognized cultivar, and its counterpart cultivated in Japan, Shinano walnut (Juglans regia L.). The results showed that Oni walnut and Hime walnut contained significantly higher protein and minerals and lower lipid content than conventional cultivars. However, both Oni and Hime walnuts contained higher ratios of unsaturated fatty acids in total fatty acids. This study offers novel insights into the nutritional components of Oni and Hime walnuts, contributing to a deeper understanding of their nutritional value and potential applications as unique native walnut species. The findings of this study highlight the relationship between the different types of walnut species and their nutritional composition, and the value of native walnuts used in local cuisine, and will lead to new developments in functional foods from walnut species consumed around the world. It will contribute to the development of functional and processed foods by increasing the production of native walnut species, which are rich in protein, unsaturated fatty acids and minerals and by using them in local cuisines and health-promoting foods.