The Yakuinsha Shrine that stands within the temple precinct originated from the Seyaku-in Temple of Heian-kyo City that stood in this area during the early Heian period and was revered for the Shinto kami Yakuin Inari but was later merged with Joko-ji Temple's Dakiniten-do hall in 1877.
境内の薬院社は、平安時代初期にこの付近にあった平安京の施薬院に由来し、薬院稲荷として崇敬をあつめてきたが、明治11年（1877年）に城興寺陀枳尼天堂に合祀された。