It is challenging for individuals to decide and select healthy foods. Recently, some countries in the world have developed nutrient profiling models, which are ranking and/or classifying foods based on their nutrient composition. However, evaluation on foods by using this concept has not been well investigated and applied in Japan to date. Therefore, by utilizing a model, we ranked foods in Standard Tables of Food Composition in Japan 2015 edition. The Nutrient Rich Food Index 9.3 (NRF9.3) for listed foods in Japanese Standard Table was calculated based on 9 nutrients to encourage and 3 nutrient to limit (per 100 kcal). Among the food groups, NRF9.3 indexes decreased in the order of seaweeds, vegetables, mushrooms, beans. Furthermore, in the same food groups, NRF9.3 indexes could clarify nutrient rich foods versus nutrient poor foods. In conclusion, NRF9.3 index would be useful in selecting alternative, more nutrient-rich foods from similar food groups when purchasing foods.