In 874, a Buddhist monk Shobo, who is known under his posthumous name of Rigen Daishi (the Great Master of Holy Treasures), built a hermitage to which Kannon (Avalokitesvara) statues of Juntei and Nyoirin were dedicated on the top of the Kamidaigo mountain where he discovered a well of the spiritual water named Daigo through an inspiration from a local god Yokoo Daimyojin. This is the origin of Daigoji temple. After a while pious supports of Emperor Daigo (897-930), Suzaku (930-46), and Murakami (946-67) contributed to development of Daigoji temple complex. In 907, for instance, the Yakushi hall was constructed to fulfill the imperial wish of Emperor Daigo. The temple complex of Kamidaigo (the upper part of Daigo) was completed by construction of the Godai hall. Consequently a plan of the Shimodaigo (the lower part of Daigo) complex was carried on. The Sakyamuni hall built in 926 and the five-storied pagoda built in 951 were consisted of the prototype of the Shimodaigo temple complex.

Since then Daigoji has played an important role as a main temple of Shingon school Ono branch in a history of Japanese Buddhism. Moreover, it might be worthwhile to note that many politicians in power have had a close family relationship with this temple. For instance, the linage of Minamoto Toshifusa, called Daigo Minamoto family, were the heads of this temple for many generations. Minamoto Toshifusa is known for having seized power instead of Fujiwara family in the late Heian period. When his son Shokaku was the head of the temple, the temple complex of both Kamidaigo and Shimodaigo was more developed and the Sanboin was constructed in 1115. From his time on Daigoji temple had enjoyed its prosperity. However, Daigoji temple suffered from several fires. The fire especially caused by Onin and Bunmei wars in Kyoto city destroyed the Shimodaigo complex except the five-storied pagoda. It is fortunate that nowadays we can see the pagoda built in 951. In Kamidaigo complex the Juntei hall is well known as the eleventh place of the pilgrimage in the Western part of Japan and the Godai hall is as the center of the Godai-san faith.

From the end of the Heian to the Kamakura period, the political system changed a lot. However, Daigoji temple retained a position as a center of Shingon school Ono branch and its doctrinal studies. In order to describe a history of Daigoji temple, first of all, Keien edited Daigo zojiki in 15 rolls. As the achievements of the doctrinal studies at that time, there remain many paintings of Esoteric Buddhism, iconographical drawings and so on, which are still invaluable source materials for the scholars.

In Nanbokucho period, the conflict between Northern and Southern Courts affects Daigoji temple as well. Koshin (bishop Mongan) had a contact with Emperor Godaigo in Southern Courts, while Kenshun had with Ashikaga Takauji, the supporter of the Northern Courts. Daigoji temple has several documents which reflect the political tensions at that time. However, an intimate contact with a person in political power enabled Daigoji to restore and develop its temple complex. For instance, it is worthwhile to refer to Manzei Jugo in the beginning of the 15th century and Gien Jugo in the end of the 16th century.

he detail diaries written by the both show their diplomatic activities. It should be noted, however, that corroborative descriptions and colophons in the diaries prove that their activities intended to preserve cultural assets in Daigoji temple. Incidentally, Gien Jugo is also well known for his organization of the gorgeous Hanami (cherry blossom viewing) party for Toyotomi Hideyoshi, which glorifies the latest life of the great hero of the age.

In Edo period, the shognate permitted Shugendo (the mountain asceticism, also called Yamabushi) practiced in Sanboin from Rigen Daishi, who is also well known for its re-founder, with an official name Tozanha. Since the entrance of the head priest Koken of Daigoji into the Omine mountain in Nara the Daigo tradition has penetrated into Shugendo more and more. To commemorate this tradition, the event called Hanagu nyubu shugyo (Practice to enter the Omine mountain to offer flowers) is held by the head priest of Sanboin in the beginning of June.

The social confusion in the end of Edo period and the new political system after Meiji Restoration brought about the reformation of the religious system of Japanese Buddhism. Many satellite temples of Daigoji corrupted as happened in other Buddhist schools. There remained a few satellite temples and Daigoji temple complex. At present most of the main buildings are designated as national treasures or important cultural assets.

The treasures in Daigoji which amount to more than a hundred thousand are preserved in Reihokan. Some of them are exhibited to the public in spring and autumn.