Prince Ōama, as Emperor Tenmu, was responsible for moving the temple from Otsu back to Asuka in 672.

The Fujiwara capital was built during this time on the Chinese model,[3] with hopes of improving economic stability and centralization of government as well as a strong military.

Yakushi-ji was commissioned by Emperor Tenmu in 680 as an offering for the recovery from illness of his consort, who succeeded him as Empress Jitō.

This act of building temples in devotion to Buddhist figures was a common practice among Japanese nobility after Buddhism was first imported from China and Korea.

Emperor Shōmu instigated the construction of the "Seven Great Temples": Tōdai-ji, Kōfuku-ji, Gangō-ji, Daian-ji, Yakushi-ji, Saidai-ji, and Hōryū-ji.

The East Pagoda (東塔, Tō-tō), completed in 730 during the Nara period, is the only original 8th-century structure at Yakushi-ji.

[1] The structure stands at 34 metres (112 ft), and is regarded as one of the finest pagodas in Japan, representing the architecture of the Hakuhō to Tenpyō periods.

The East Pagoda replicated styles at the Heijo Yakushiji, with 12 granite column foundation stones found during excavations, while the West Pagoda demonstrated signs of being constructed during the early Nara period, after the capital had been moved, and has a different style.

[2] Yakushi was first worshipped as a "Medicine Buddha" by members of the wealthy and powerful elite, who prayed to him for relief from illness for themselves or their loved ones.

It was not until later that the Tendai sect developed a cult around him on the basis that he could bring health and prosperity to all human beings.