In the late 12th century, Fujiwara no Sukeyori, a descendant of Fujiwara no Hidesato in the 9th generation, received the title of Dazai Shōni (equivalent to that of vice-governor of the military government of Kyūshū) from Shōgun Minamoto no Yoritomo, and the title became the family name.

The clan played an important role in the region as early as the Muromachi period, when it helped suppress opposition to the Ashikaga shogunate's control of Kyūshū.

The clan initially aided Ishida Mitsunari against Tokugawa Ieyasu in the Sekigahara Campaign in 1600.

Though regarded as tozama daimyō ("outside" lords), and assigned particularly heavy corvée duties, the Nabeshima were allowed to keep their territory in Saga, and in fact had their kokudaka increased.

The clan's forces served the new Tokugawa shogunate loyally in the years which followed; they remained in Kyūshū during the 1615 Osaka Campaign as a check against a possible rebellion or uprising by the Shimazu clan, and aided in the suppression of the Shimabara Rebellion of 1637.