Yakushiji Motonaga served as a bushō during the Sengoku period.  He was a senior retainer of the Hosokawa-Keichō family and the deputy military governor of Settsu Province.

Motonaga served Hosokawa Katsumoto, the kanrei, or deputy shōgun, and received one of the characters from his name, adopting the name of Motonaga.

During the Ōnin-Bunmei War, he followed Katsumoto, the supreme commander of the Eastern Army, and fought in battles against the Western Army across Settsu and Tanba provinces.  Owing to his contributions, Motonaga was appointed as the deputy military governor of Settsu.  After the death of Katsumoto, he served Hosokawa Masamoto.

Under Masamoto, Motonaga governed Settsu, serving as a mainstay of the Hosokawa-Keichō family.  He eliminated kokujin, or provincial landowners, in Settsu including Suita Tokimichi and the Ibaraki clan who were opposed to the Hosokawa.  Later, although not formally recognized, Motonaga allocated a portion of his authority to his younger brother, Yakushiji Nagamori.  Nagamori was called the deputy military governor of the outlying districts.

Motonaga died on 12/17 of Bunki 1 (1501) and was succeeded by his son, Yakushiji Motokazu.  Under another theory, Motokazu and Yakushiji Nagatada were the natural sons of Motonaga’s younger brother, Yakushiji Nagamori, and adopted by Motonaga.