The Shin Buddhist path was founded by Shinran Shonin (1173-1262) during the Kamakura period, and in several centuries grew into one of the largest and most influential schools of Buddhism in Japan, a position it maintains today. The Hongwanji temple is the headquarters of the Hongwanji denomination of Shin Buddhism (Jodo Shinshu Hongwanji-ha), and is known as Nishi (lit. "West") Hongwanji.

Origins
The Hongwanji developed from a modest temple built at the site of Shinran Shonin's mausoleum. After his death, his cremated remains were interred at Otani in the eastern hills of Kyoto and marked by a simple stone obelisk.

Many followers came to pay their respects, particularly from the distant Kanto region (now the Tokyo area), and in 1272, with their support, Shinran's daughter, Kakushinni, had his ashes moved to the grounds of her residence at Yoshimizu, slightly to the north. There, a hexagonal chapel was built and an image of Shinran enshrined.

Several years later, with the death of her husband, title to the residence passed to Kakushinni, allowing her to determine the future of the chapel, and in 1277, she dedicated her property to the Shin movement as a permanent mausoleum, to be tended by a person of Shinran's lineage. The chapel and land became known as the Otani Mausoleum (byodo) and was supported by followers in the Kanto area.

The first intendant of the mausoleum was Kakushinni's son, Kakue, and in 1310 he was succeeded by his son, Kakunyo. Kakunyo elevated the status of the mausoleum by gaining recognition for it as a temple, and further sought to make it the center of the Shin movement. It was he who adopted the name Hongwanji (lit. "Temple of the Primal Vow").

In 1336, the Otani Mausoleum was burned during warfare between Ashikaga Takauji and Emperor Godaigo. Kakunyo rebuilt it, not as a hexagonal chapel, but as a regular temple. In succeeding generations, the Hongwanji developed the present format of two halls, the Founder's Hall and the Hall of Amida Buddha. Factions formed among Shin followers, however, and most of the ten Shin denominations arose during this period, around central temples in various parts of the country. It was not until the time of Rennyo that the Hongwanji became the center of the Shin tradition, independent from the Tendai organization.