Initially a large complete Shichidō garan temple, it suffered from fire damage and deteriorated during the Heian period.

The Hon-dō, the principal image of Yakushi Nyorai and eleven statues of the Twelve Heavenly Generals have been designated by the Ministry of Education, Culture, Sports, Science and Technology of the government of Japan as National Treasures.

[2] According to records at Tōdai-ji, Shin-Yakushi-ji was founded in March 747 as Kōyaku-ji (香薬寺) by Empress Kōmyō wishing for the recovery of her husband, Emperor Shōmu, who suffered from an eye ailment.

She had a large nine bay temple hall (Kon-dō) built and statues of the Seven Buddhas of Healing (七仏薬師, shichibutsu yakushi) enshrined in it.

[4] The Twelve Heavenly Generals surrounding the main image of Yakushi Nyorai were transferred to the hall from the ruined Iwabuchi-dera (岩淵寺) located not far from Shin-Yakushi-ji on the foot of Mount Kasuga.

In the Kamakura period the priests Jōkei (貞慶) (posthumous name: Gedatsu Shōnin) and Myōe restored the temple after the general decline.

The Kon-dō from the time of founding differed from the present main hall in size and its position within the temple grounds.

The Hon-dō has been designated as a National Treasure and houses the main image of Yakushi Nyorai surrounded by a group of Twelve Heavenly Generals.

[2][3] The upper parts of the main pillars in the East Gate (東門, tōmon) are split in two, held by solid-board frog-leg struts (板蟇股, itakaerumata).

The building features a flared, skirt-like lower portion, also known as hakamagoshi (袴腰) style, which became popular in the late Heian period and thereafter.

One day, a child with superhuman strength who had joined the temple, decides to kill the ogre and lies in wait in the belfry.

The present image is probably not one of those that had been installed in the original Kon-dō and were made in a hollow dry lacquer (脱活乾漆造, dakkatsu kanshitsu zukuri) technique.

[8] Generally it is considered to be a work of the end of the 8th century and a good representative example of early Heian period wooden sculptures.

It is cut from a single Hinoki tree and neither paint nor lacquer have been applied to the wood except for some colour to indicate facial features.

[2] [3][6] The Nara period, roughly life-size standing group of Twelve Heavenly Generals from 729–749 is the oldest extant in Japan.

Beards were drawn with ink, cloths and armour painted in bright colors and gold foil applied in places.

In a collaboration between Shin-Yakushi-ji and the Department of Buddhism at Minobusan University, the whole group of Twelve Heavenly Generals was scanned in three dimensions in 2001 and 2002.