It was developed by Hosoda Yasubei during Bunkyū years (1861 - 1863) in the Edo period. He established a wagashi store which was named from his childhood name, Eitaro. That store continues in Tokyo yet.
Originally amanattō was called amananattō, the name was abbreviated to amanattō after World War II. The resemblance of the name to the name of the fermented bean dish nattō is only coincidental.
In Hokkaidō, amanattō is used for cooking the sekihan. For this reason, unlike other areas, the sekihan of Hokkaidō is a little sweet.