The temple was founded in 1282 by a Chinese Zen monk at the request of the then ruler of Japan, the regent Hōjō Tokimune after he had repelled a Mongolian invasion in the period 1274 to 1281. Tokimune had a long-standing commitment to Zen and the temple was intended to honour those of both sides who died in the war, as well as serving as a centre from which the influence of Zen could be spread. According to the records of the time, when building work started a copy of the Sutra of Perfect Enlightenment (in Japanese, engaku-kyō) was dug out of the hillside in a stone chest during the initial building works, giving its name to the temple.
The fortunes of the temple have waxed and waned over the centuries. Its present form is owed to the Zen priest Seisetsu, who reconstructed and consolidated it towards the end of the Edo era. In the Meiji era, Engaku-ji became the chief centre for Zen instruction in the Kantō region; Kosen Roshi and Soyen Shaku were successively abbots in this period, and Daisetz Teitaro Suzuki was a student under them. Zazen courses are still held in the temple.
