In the Middle Ages (from the end of the twelfth century to the end of sixteenth century in Japanese history), Kiko-ji Temple became a branch temple of Kofuku-ji Temple, and more precisely, it belonged to Ichijo-in (a temple where priests from families of emperors' chief advisors lived), a sub-temple of Kofuku-ji Temple.
中世には興福寺の末寺となり、直接には興福寺の塔頭の一つであった一乗院に属した。