The origins of this shrine date to around 1274. An immediate vassal of the Kamakura Shogunate, Kawano Michiari (河野通有), was about to lead troops during the second Mongol invasion of Japan and he prayed for success at a local shrine, Oyazumi Jinja. His prayers were answered and he was successful at what became known as the Battle of Koan (弘安の役) in 1274. He subsequently had a dream in which he was instructed to build a jinja in Toshima district, Musashi Province enshrining the spirit of Oyazumi Kami. This he did. The Oyazumi Kami enshrined through the bunrei process was the one at Oyazumi Jinja in Shikoku.   

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In 1650 the shrine was forced to relocate by the Bakufu and it moved to Kanesugimura Village in what is now Negishi in Taito-ku. In 1710 it was again forced to move, this time to what is now Kotobuki in Taito-ku. This is the present day Mishima Jinja. However, this left the residents of Kanesugumura Village without a jinja and after some discussion it was decided to again enact the bunrei process and the current Motomishima Jinja was thus founded. In the same way another Mishima Jinja was founded in Taito-ku, this one in Shitaya.​