The origins of Sanzen-in Temple lie in a temple named Enyu-bo built on Mt. Hiei during the time of Saicho in the 8th century, which was later relocated to Sakamoto (present day Otsu City) on the eastern base of Mt. Hiei and then moved several more times before arriving at its current location in 1871.
三千院は8世紀、最澄の時代に比叡山に建立された円融房に起源をもち、のちに比叡山東麓の坂本(大津市)（現・大津市）に移され、たび重なる移転の後、1871年（明治4年）に現在地に移ったものである。