As an ally of Oda Nobunaga, Hashiba Hideyoshi received Odani-jo, but since it was a mountain castle it was difficult for him to govern his lands. He then moved to the Kunitomo village and built his own castle there in 1575. He borrowed the character for naga from Nobunaga's name and renamed the area Nagahama.

After the battle of Shigatake in 1583 the castle was taken over by Yamanouchi Kazutoyo and after the Battle of Sekigahara in 1600 it was ruled by Naito Nobunari. Nagahama-jo was demolished in 1615 because if the Tokugawa law of "one castle per province." Some of Nagahama-jo's structures and moat walls were moved to Hikone-jo.