As with other Tendai Sect Monzeki Temples (Shoren-in Temple and Sanzen-in Temple), the origins of Myoho-in Temple are believed to lie in a bo (small temple) situated atop Mt. Hiei and the first chief priest is thought to have been Dengyo Daishi Saicho (767-822).
天台宗の他の門跡寺院（青蓮院、三千院など）と同様、妙法院は比叡山上にあった坊（小寺院）がその起源とされ、初代門主は伝教大師最澄（767－822）とされている。