The temple was built by the widow to Hideyoshi, warlord. Gold-relief lacquerware called Maki-e is exhibitied here.The origin of this temple lie in the volatile Momoyama,16th century period. Nene, the wife of Toyotomi Hideyoshi, built Kodaiji and the North Garden, Kita-teien at Fushimi castle for her husband. When he died, the garden was transferred to Kyoto from Fushimi. Construction of the temple, Kodai-in, began in 1603 with some garden work being done two years later.

The name was changed to Kodaiji in 1606. Entokuin, built in 1627, is actually a subtemple of the Kodaiji complex, located across the street. The narrow street that passes between Entokuin and Kodaiji is still called Nene Street.