It was centered around Funai Castle in what is now the city of Ōita and was ruled by the fudai daimyō Ogyū-Matsudaira clan for most of its history.

The Ōtomo were saved by Toyotomi Hideyoshi's 1586-1587 Kyūshū campaign and were allowed to reclaim Bungo province as their territory.

Bungo was divided into small fiefs At the Battle of Sekigahara in 1600, Takanaka Shigetoshi, a cousin of the famous Takenaka Hanbei, initially sided with the Western Army and participated in the Siege of Tanabe, but later defected to the Eastern Army, and was rewarded by Tokugawa Ieyasu with an increase in his estates from 10,000 koku in Bungotakada to 20,000 koku in Funai.

In 1658, Yoshiakira's nephew-in-law (the son of his legal wife's brother), Matsudaira Tadaaki, the daimyō of Bungo Takamatsu Domain was transferred to Funai.

Throughout the remainder of the Edo period, the Ogyū-Matsudaira clan continued to rule Funai for ten generations until the Meiji restoration.