In the Heian period, as many other temples in the Omi Province, Hyakusai-ji Temple also fell within Enryaku-ji Temple on Mt. Hiei and became a temple of the Tendai sect.
平安時代には、近江国の多くの寺院と同様、比叡山延暦寺の勢力下に入り、天台宗の寺院となっている。