Higashi Hongan-ji a été fondé au début du XVIIe siècle.

Tokugawa Ieyasu deliberately split the powerful Jōdo Shinshū sect in two in 1602, creating Higashi Hongan-ji to weaken the original temple's political influence after decades of armed resistance.

The temple burned down four times during the Edo period. After the devastating 1864 fire during the Kinmon incident, rebuilding didn't start until 1879 due to political turmoil from the Meiji Restoration.

Locals affectionately call the two Hongan-ji temples 'Onissan' (Honorable Mr. West) and 'Ohigashisan' (Honorable Mr. East), treating them like friendly neighbors rather than grand religious institutions.