Yūki Naotomo served as a bushō during the late Muromachi period.  Naotomo was the sixth head of the Shirakawa-Yūki clan.  The Shirakawa-Yūki were an illegitimate branch of the Shimōsa-Yūki clan governing the Shirakawa area in the southern portion of Mutsu Province during the Sengoku period.

Naotomo was born as the son of Komine Tomochika, the fifth head of the Komine clan.  Later, he was adopted by Yūki Ujitomo, the fifth head of the Shirakawa-Yūki, and inherited the headship of the clan.  In 1432, he was invested with the title of Master of the Office of Palace Repairs.  In 1438, he obtained the support of the Muromachi bakufu during the Eikyō Conflict which enabled him to extend his authority over clans in the southern portion of Mutsu Province and in the northern Kantō.

In 1458, Naotomo offered protection to Utsunomiya Hitotsuna who was banished from the Kantō by Ashikaga Shigeuji (the Koga kubō) during the Kyōtoku War.  Later that year, he was ordered by the bakufu to subdue Shigeuji and to deploy with Ōsaki Norikane, the Oushū tandai, or commissioner of Mutsu, but he did not deploy to the Kantō.  Instead, in 1472, Naotomo served as a mediator between Nasu Akisuke (the head of the Upper Nasu family) and Nasu Sukezane (the head of the Lower Nasu family) which families were opposed to one another following a split of the Nasu clan in Shimotsuke Province dating back to the 1440’s.  Naotomo further intervened in disputes in other families, acquiring landholdings.  During an internal conflict in the Ashina clan, he came to the support of Ashina Moriakira.  The Shirakawa-Yūki attained their period of most influence in the era of Naotomo.

In 1466, Naotomo transferred the headship of the clan to his son, Yūki Masatomo. and entered the priesthood, adopting the name of Dōtō.  Nevertheless, he continued to serve as the primary authority in the clan.  In 1481, he attended a renga event hosted by Masatomo at the Kashima Shrine below Shirakawa Castle.