Shoden-ji Temple is believed to have originated with a temple founded in 1268 by Gottan Funei, a disciple of Togan Ean, in Karasuma Imadegawa before being relocated to its current site in 1282 with the assistance of Tsunehisa MORI of Kamo-sha Shrine, then the temple became prosperous.
1268年、東巌慧安が師の兀庵普寧（ごったんふねい）を開山として烏丸今出川に創建したのがこの寺の始まりとされ、1282年に賀茂社の森経久の援助を受け、現在地に移り寺運は興隆した。