Kobo Daishi founded the temple after Dainichi Nyorai appeared in a purple cloud during his training, declaring 'This land is a sacred place.' He carved the deity's statue on the spot and built the temple immediately.

Dainichi-ji a été incendié durant l'ère Tensho par les forces de Chosokabe Motochika, puis reconstruit au début de l'époque d'Edo.

The temple's principal image switched in the Meiji era: an Eleven-Faced Kannon from the neighboring shrine replaced the original Dainichi Nyorai statue, which was demoted to a side position after centuries as the main deity.

Dainichi-ji est le temple n° 13 du pèlerinage des 88 temples de Shikoku à Tokushima.