The family made its formal residence in the Kitayama (northern mountains) area of Kyoto; the residence was likewise called Saionji, meaning "Western Garden Temple." Thus the family came to be sometimes known as the Lords of Kitayama; when Ashikaga Yoshimitsu became shogun in 1368, he coopted the site for his Kinkakuji, thus laying some claim to a connection to the Saionji and to their prestige as Lords of Kitayama.
Saionji Sanekane joined the family to the Daikakuji line of the Imperial family, having become involved with the daughter of Emperor Go-Daigo or Emperor Kameyama and siring a son, Saionji Kinhira. Several decades later, in the time of Saionji Kinmune, the Kamakura shogunate came to an end, and the Saionji were dismissed from their post as Kantō Mōshitsugi. Kinmune helped hide the persecuted Hōjō Yasuie and, in the wake of the death of Emperor Go-Daigo, helped plot to set Emperor Go-Fushimi on the throne. His schemes revealed by his younger brother Saionji Kinshige, Kinmune was arrested and executed. During the Nanboku-chō period (1336-1392) which followed, in which the two Imperial lines jousted for power, Kinmune's son Saionji Sanetoshi served the Northern Court as Minister of the Right (Udaijin), restoring the prestige of the family's name.
A Saionji family is known to have existed in Edo period (1600-1868) Kyoto, as producers of biwa. Saionji Saneharu was made Minister of the Left (Sadaijin), and gained influence and some financial support through connections to the Hosokawa and Nagaoka clans. Towards the end of the Edo period, Saionji Kinmochi was adopted into the family from the closely related Tokudaiji branch of the Fujiwara clan. Kinmochi lived through the Meiji Restoration, becoming one of the genrō, or elder statesmen who were a part of the original Meiji government at its beginning. He subsequently held a number of Cabinet posts, becoming Prime Minister of Japan in 1906.
As members of the kazoku (Western-style system of peerage), the Saionji maintained a considerable degree of prestige, and continued to be close to the world of politics, through the end of World War II, when the kazoku were dissolved. The family continues today, and Saionji remains a not uncommon Japanese surname.