Sanzen-in Temple is the oldest of the Three Monzeki Temples of the Tendai Sect and is said to originate from a temple named 'Enyu-bo' built in Toto Minamidani (a district located within Mt. Hiei) and dedicated to the principal image of a statue of Bhaisajyaguru carved by Saicho himself when he founded the Mt. Hiei Enryaku-ji Temple in 788.
三千院は天台三門跡の中でも最も歴史が古く、最澄が延暦7年（788年）、比叡山延暦寺を開いた時に、東塔南谷（比叡山内の地区名）に自刻の薬師如来像を本尊とする「円融房」を開創したのがその起源という。