In 1272, ten years after Shinran's death, a mausoleum rather than a grave was built to enshrine his ashes together with his image. This mausoleum was moved on various occasions.

However, after the division into Higashi and Nishi Honganji in 1602, Ōtani Mausoleum was finally constructed at its present location in 1670, though later it was rebuilt along with halls at the end of the 17th century.

In 1745, Shōgun Tokugawa Yoshimune donated about 33,000 square meters (8 acres), by which Ōtani Mausoleum was able to expand.