According to temple tradition, it was founded in 860 AD by the priest Ennin, who is better known by his posthumous name, Jikaku Daishi (慈覺大師). In 847 AD Ennin returned to Japan from studies in Tang dynasty China and in 854 AD he became the chief priest of the Tendai sect at Enryaku-ji on Mt. Hiei near Kyoto. Risshaku-ji was founded as a branch temple of Enryaku-ji by the order of Emperor Seiwa, and to this day the ritual fire brought from Enryaku-ji is still burning in the main temple. The exact date and circumstances of the foundation of the temple are uncertain, but it dates to at least the early Heian period based on dating of the oldest of its surviving wooden statuary. The temple has a long-standing tradition that it houses the grave of Ennin in a cave within the temple grounds. Although Enning died on Mount Hiei in 864 AD, and there is no record that his remains were transferred here, Ann archaeological investigation in 1948 found a gold-leaf encrusted casket containing five sets of human remains and fragments of a Heian period wooden statue of Ennin within the cave. The temple developed into the major Heian period center for Buddhism in Dewa Province (now Yamagata and Akita prefectures).[1]

The temple was patronized by the Kamakura shogunate and grew in territory. It was rebuilt after a fire in the mid-13th century and was converted to Zen Buddhism. The current Min Hall, known here as the Konpon-chūdō was rebuilt in 1356 by Shiba Kaneyori, lord of Yamagata Castle, who also returned it to the Tendai sect. It was visited by the artist Sesshū Tōyō in 1482, who made many sketches of its precincts. The temple was burned down again during the wars of the Sengoku period, but was restored by the Date clan and the Mogami clan. Under the Edo Period Tokugawa shogunate, it was awarded estates with a kokudaka of 1420 koku for its upkeep.[1]

Yama-dera is where the well-known haiku poet Matsuo Bashō wrote his famous haiku "ah this silence / sinking into the rocks / voice of cicada" in 1689. A museum of Basho's writings and paintings and other related art, the Yamadera Basho Memorial Museum, is a short walk up the hill on the opposite side of the steep valley. In 1996, the Ministry of the Environment selected the cicadas of Yama-dera as one of the 100 Soundscapes of Japan.[2]