When Toyotomi Hideyoshi became lord of Nagahama Castle in 1573 and developed the town, he restored this shrine. To celebrate the birth of his eldest son Tsurumatsu, he had children's kabuki performed on hikiyama festival floats — said to be the origin of today's Nagahama Hikiyama Festival. Although Hideyoshi's tenure as lord of Nagahama was brief, the townscape and rites he organized have been carried on for over 400 years and form the foundation of Nagahama's townsmen culture.

Nagahama Hachimangu was founded by Minamoto no Yoshiie, who enshrined a divided spirit of Iwashimizu Hachimangu here — the tutelary deity of the Minamoto clan. After establishing the Kamakura shogunate, Yoritomo venerated this shrine and donated temple lands to support it, making devotion to Hachiman a spiritual cornerstone of his warrior government.