It was developed by Hosoda Yasubei during the Bunkyū years (1861–1863) in the Edo period. He opened a wagashi store in Tokyo, which he named for his childhood name: Eitaro. This store continues to operate.
Originally amanattō was called amananattō(甘名納糖?); the name was abbreviated to amanattō after World War II. The resemblance of the name to the fermented bean dish nattō is coincidental.