During the Nanboku-cho period, this major Shingon temple served as the Southern Court's imperial palace for Emperor Go-Daigo and Emperor Go-Murakami. Its seated Dainichi Nyorai is a National Treasure.

Kongoji, set in the mountains close to the Kusunoki stronghold of Chihaya Castle on Mount Kongō, was a temple held in particular reverence by the Kusunoki clan. During the Nanboku-chō civil war, Emperor Go-Murakami — who succeeded to the Southern Court throne after Go-Daigo's death — established his temporary palace here, making it both a political and spiritual center for the cause Masashige had died to uphold. Sharing the name "Kongō" with Chihaya Castle and Mount Kongō, this "Women's Kōya" was the hallowed temple of prayer under the Kusunoki clan's protection.