Yakushi-do Temple (also known as Ruriden) was built in 747 during the time of a major smallpox epidemic. The hall houses Yakushi Nyorai, Nikko and Gakko Bosatsu, and the Twelve Divine Generals, who protect believers of Buddha who chant the Yakushi Sutra. It is believed that during this period, when the capital was located in Nara, a monk named Gyoki visited this place and held a ceremony for drawing the eyes on the statue of Yakushi Nyorai (said to welcome the spirit) at the request of Emperor Shomu. Gyoki was also instrumental in the construction of Todaiji Temple, and he was the first person in Japan to be appointed a highest-ranked monk.

The three-storied pagoda was built in 823. The pagoda is about 25 meters tall, making it one of the tallest towers to be build in Japan in that era. In the past, Shakubuji Temple had an area that stretched 1 Ri (approx. 4 kilometers) north-to-south and 2 Ri east-to-west. This temple is one of the most influential in the country, with many Gakuryo (monks studying Buddhism) there and more than 70 smaller temples in the mountains.