Ishiyamadera is located near the southern end of Lake Biwa, on the right bank of the Seta River, the only river that flows out of Lake Biwa. The main hall is built on a huge bedrock called wollastonite (Ishiyamadera wollastonite), which is a national natural monument, and this is also the origin of the temple name.

During the Middle Ages, Ishiyama-dera was revered by Taira clan Minamoto no Yoshitsune, Kamakura shogunate Minamoto no Yoritomo, Hojo Tokiyori, and others, and prospered to the extreme. In addition, Minamoto no Yoritomo made the Nyoirin Kannon of Ishiyama-dera the principal guardian deity of the shogunate.

In the early modern period, Ishiyama-dera Temple was revered by Toyotomi Hideyoshi and Tokugawa Ieyasu, and many temple treasures were donated.

The pagoda is designated as a national treasure.