According to temple tradition, Hojo Tokiyori (1227–1263), the fifth regent of the Kamakura shogunate, restored Saimyoji during his tenure as a lay monk known as Saimyoji Nyudo. Tokiyori was one of the era's most devoted Zen patrons, founding and supporting many temples including Kenchoji (1253) and Enjoji (1255). His connection to Musashi-Kosugi, together with the later Edo-period Kosugi Goten (a Tokugawa shogunal rest-stop built adjacent to the temple), attests to the site's continued importance as a waystation for the warrior class.

Temple tradition holds that it was founded by Jikaku Daishi (Ennin) on his Eastern pilgrimage and restored by Saimyoji Nyudo (Hojo Tokiyori) in the Kamakura period.