The temple was later relocated to the center of Kyoto at the end of Heian period (12th century) during the reign of Cloistered Emperor Goshirakawa, where it was temporarily located at Ayanokojikosaka (assumed to have been to the south-west of Yasaka-jinja Shrine in Higashiyama Ward, Kyoto City) before being moved to its current location on the former site of Hojuji-dono Palace in the early modern period.
その後、平安時代末期（12世紀）、後白河法皇の時代に洛中に移転し、一時は綾小路小坂（現在の京都市東山区・八坂神社の南西あたりと推定される）に所在したが、近世初期に現在地である法住寺殿跡地に移転した。