Per the Kojiki and the Nihon Shoki, Amaterasu's grandson Ninigi descended from the heavens to Mount Takachiho, and resided in what is now Saito.

The area was densely populated in the Kofun period and has the largest accumulation of ancient burial mounds in Japan.

During the Muromachi period the Ito clan ruled the area from their stronghold at Tonokōri Castle in the southern part of the city.

Following the Meiji restoration, the area was organized into villages within Koyu District, Miyazaki on May 1, 1889, with the creation of the modern municipalities system.

In terms of national politics, the city is part of the Miyazaki 2nd district of the lower house of the Diet of Japan.