In 1282, the eighth regent Tokimune founded Engakuji to memorialize all who died in the Mongol invasions, regardless of side. He invited Mugaku Sogen from Song China as founding abbot. Tokimune himself practiced Zen diligently and was buried here after his death at age 34.

Yoritomo especially revered this shrine, positioned in the demon gate (northeast) of the Okura shogunate, as a protector of his government. At this shrine to Michizane, the god of learning, Yoritomo prayed not only for military fortune but also political stability. It preserves the oldest shrine architecture in Kamakura.

Engakuji was founded in 1282 by Hojo Tokimune — Takatoki's great-grandfather and the eighth Hojo regent — to memorialize the war dead of the Mongol invasions, with the Song Chinese master Mugaku Sogen as founding abbot, and thereafter served as the spiritual pillar of the Hojo Tokuso lineage. As fourteenth regent and Tokuso heir, Takatoki practiced Zen at Engakuji from his youth and revered the successive abbots who inherited Mugaku Sogen's dharma line. On the 22nd day of the 5th month of 1333, Takatoki committed suicide with his clan at Tosho-ji during Nitta Yoshisada's assault on Kamakura, ending the Kamakura shogunate. Even after the fall of the regime Engakuji continued to perform memorial rites for the Tokuso family, and in the inner precinct of Butsunichi-an the Hojo lineage stupas (hokyo-into) preserve the memorial pagodas of three generations — Tokimune, Sadatoki, and Takatoki — side by side. A Hojo memorial service is observed each year around the 22nd of May, sustaining the spiritual bond between the Tokuso bloodline and Engakuji.