In the beginning of the Meiji period (1868–1912), the movement to Westernize and modernize Japanese society put the country’s traditional culture, antiquities, sacred temples and shrine treasures at risk of damage or destruction. In order to protect Japan’s endangered cultural properties, the government committed in 1889 to build three national museums, in Tokyo, Kyoto, and Nara. The Kyoto National Museum opened in 1897 under the name Imperial Museum of Kyoto.

In 2014, the museum opened a new wing, the Heisei Chishinkan, to house exhibitions of its extensive collections, comprising over 12,500 significant works of art—including ceramics, archaeological artifacts, painting, sculpture, calligraphy, textiles, metalwork, lacquer, and other genres. The collections comprise not only works owned by the museum but also treasures from temples, shrines, and private collections, which are entrusted to the Kyoto National Museum on long-term loan.