In 1952, the government purchased the premises of the former headquarters of Nikkatsu Corporation in Kyobashi, Chuo-ku. In June that year, The National Museum of Modern Art was established as an institution governed by the Ministry of Education. The architect Kunio Maekawa directed the refurbishment and the Museum was opened that December. On two later occasions, neighbouring premises were purchased and the Museum was further enlarged and reformed.

Due to the growth of the Museum Collection and the expansion of special exhibitions, the display of works gradually got restricted. Just when the Museum was considering possibilities of moving, Mr.Shojiro Ishibashi,who was a trustee from the founding of the Museum, offered to donate a new building. Thanks to this donation, it was decided that a new wing would be constructed in Kitanomaru Koen. The new building was designed by Yoshiro Taniguchi and opened in June 1969.

After 30 years since moving to the present building, it became necessary to update the facilities to meet social demand. For two and a half years from July 1999, the Museum was closed and underwent large-scale extension and renovation designed by Sakakura Associates. The exhibition galleries were enlarged, a library allowing access to the public, a restaurant and museum shop were newly established, and lounge space was increased. In addition to improving the environment for viewing the works of art,construction work to make the building more earthquake-proof was carried out. The renovation work was completed in August 2001 and, in January 2002, an exhibition entitled The Unfinished Century: Legacies of 20th Century Art was held to commemorate the renewal and restart of activities anew.