It originated in 1311, when Joa Shinkan was given Gidarin-ji Temple, which was then located at Shijo Kyogoku, by the Retired Emperor Gofushimi as a reward for his contribution to the delivery of Kogimonin Fujiwara no Yasuko, the retired Emperor's nyogo (consort), and renamed it Konren-ji Temple.
1311年（応長元年）、浄阿真観が後伏見上皇の女御広義門院藤原寧子の出産に際し効があったことから、上皇から四条京極にあった祇陀林寺を賜り金蓮寺と改めたことに始まる。