The 8th Muromachi Shogun, ASHIKAGA Yoshimasa (1436-1490) started construction of a villa, Higashiyama-dono at the foot of Mt. Higashiyama in the year 1482. He moved in Higashiyama-dono next year. Togu-do building was completed in 1486. Ginkaku was completed in 1490 just after Yoshimasa passed away. The villa was changed into a temple, Jisho-in, in accordance with his will. Muso Soseki was nominated as the founder of the new temple. In 1491, the name of the temple was changed to Jisho-ji.

Sometime between 1550 and 1561, all the buildings but Togu-do and Ginkaku were burned down by fires of war. The temple was dilapidated for some time.

From 1615 to 1644, large-scale repair and reconstruction was made by MIYAGI Toyomori and his grandson Toyotsugu. Sometime between 1735 and 1799, Ginshadan and Kogetsudai were installed.

In the year 1931, the ruins of Karesansui garden was excavated. In 2007, a scientific research confirmed that silver leaves have never been applied to Ginkaku. In 2008, the city of Kyoto suggested lacquering the second story of Ginkaku in original black to preserve it, but the temple declined the idea because they believed weathered walls would fit the culture of Wabi and Sabi.