Shinran, who passed away at the age of ninety on November 28, 1262, was cremated at Higashiyama Toribeno in Kyoto, and his ashes were interred at Ōtani. A mausoleum was built there, in which a figure of Shinran was enshrined. This, then, is the origin of the present Higashi Honganji.

The Ōtani Mausoleum was built through the cooperation of Shinran's daughter, Kakushinni, and his close followers in the Kantō area. The position of "caretaker" (rusu-shiki) was inherited from Kakushinni by her first son, Kakue, followed by her grandson, Kakunyo, who became the 3^rd successor. He eventually changed the name of the mausoleum to "Honganji," which then became officially recognized as a temple. Later, Honganji became affiliated with the Tendai temple Shōren-in, where Shinran had been ordained, and began to take on the traits of that particular Buddhist school, such as having a gomadan (a place on the altar to burn small pieces of wood to invoke divine help).

The 7^th successor, Zonnyo, built two halls at Honganji: the Founder's Hall (Goei-dō), in which the image of our founder, Shinran, was enshrined and Amida Hall (Amida-dō) where the figure of Amida Nyorai (Amida Buddha) was placed. Zonnyo promoted the teaching in Ōmi province (present-day Shiga prefecture) and the Hokuriku region (on the Sea of Japan).

Rennyo, Zonnyo's son, became the 8^th successor in 1457, and began to reform Honganji where "not even a single person attended," by abolishing the services and adornments of the Tendai denomination. Instead, he established the format of chanting Shōshinge and Wasan (hymns) composed by Shinran. Further, through positively introducing the teaching to Ōmi province, he was able to make connections with many followers there.

However, the Tendai monks of Mt. Hiei felt threatened by these activities and destroyed Honganji. Rennyo escaped to Ōmi province, and later began a community in Yoshizaki in Echizen province (present-day Fukui prefecture), where he continued propagation. He spread Shinran's teaching to many people, especially through easily understandable pastoral letters, called Ofumi, and by organizing local gatherings (kō).

When Yoshizaki became prosperous, discord with other established religious groups arose and political confrontations developed, resulting in the Shinshū followers' uprisings (ikko-ikki). Deploring the expansion of such conflicts, Rennyo left for Kawachi province (present-day Osaka prefecture) and spread the Nenbutsu teaching there.

Thereafter, with the aim of rebuilding Honganji, Rennyo headed for Yamashina, Kyoto. While spending six years there from 1478, he concentrated the efforts of his followers throughout the country so as to construct a temple complete with buildings including the Founder's Hall and Amida Hall. Followers, merchants and craftsmen gathered around the temple and established a town, which was described as being "splendid like the Buddha-land."

In 1532, the followers of the Hokke-shū (Nichiren denomination), who feared the expansion of Honganji's power, suddenly attacked and burned down Honganji at Yamashina. The 10^th successor, Shōnyo, fled to Osaka (Ishiyama) and established the main temple there. Just as in Yamashina, a temple town developed around Honganji.

However, around the time of the 11^th successor, Kennyo, Honganji was again faced with a crisis. Oda Nobunaga, who was aspiring to bring the whole country under his rule, demanded the possession of Osaka Honganji because of its ideal geographic and strategic location. Honganji refused and fighting began in 1570. This is known as the Battle of Ishiyama. Although Honganji confronted Nobunaga through the help of followers throughout the country and feudal lords such as Mōri, it finally made peace in 1580 and Osaka Honganji was handed over to Nobunaga.

Two years after Honganji had left Osaka, and after Nobunaga had died in the Honnōji Incident, Toyotomi Hideyoshi treated Honganji well, and donated land in Tenma, Osaka and later in Horikawa Shichijō, Kyoto. However, in 1592, right after Honganji had moved to Kyoto, Kennyo passed away and was succeeded by his first son Kyōnyo. A dispute concerning succession arose, however, in the following year, and Hideyoshi was asked to arbitrate. He decided that Kyōnyo should step down and hand over the position to his younger brother, Junnyo. Later, in 1602, Kyōnyo built another temple in Karasuma Rokujō, on land donated to him by Tokugawa Ieyasu. Thus, Honganji was split into two, caused originally by the conflict between the reconciliation (Kennyo) and resistance (Kyōnyo) factions in the Battle of Ishiyama and the temple in Karasuma came to be called "Higashi (East) Honganji."

Despite the split, Higashi Honganji and its followers established a firm foundation as a major Buddhist denomination in Japan. Buildings, including the Founder's Hall and Amida Hall, were destroyed by fire four times during the Edo period and were rebuilt each time. The present two halls were completed in 1895.

Even though Higashi Honganji repeatedly encountered tragedies throughout its history, with fires on four different occasions, each time all the denomination’s community concentrated its aspirations, and rebuilt the two halls without reducing or simplifying its scale, but rather increased the depth of their magnificence and dignity. This represents the manifestation of the religious mind of our predecessors, which seemed to well up from deep within their hearts. The existence of the two halls is irreplaceable, conveying the hardships experienced through the history of reconstruction and reminding us of our predecessors’ respect for Shinshū Honbyō, the central practicing place of our denomination.