The Board of Audit originates from a Kantokushi (Inspection Division) established in 1869 as one of the divisions of the Kaikeikan (the forerunner of the Ministry of Finance) inside the Dajokan (a previous form of the Cabinet). Through several changes in its name, such as Kensaryo (Hall of Audit) and Kensakyoku (Bureau of Audit), the Board was organized as a supervising agency for financial administration under the direct control of the Dajokan in 1880. The Board acquired constitutional status under the Meiji Constitution in 1889 and conducted oversight on public finances as an independent organ directly subordinate to the Emperor.

In 1947, with the establishment of the Constitution of Japan, the Board's subordination to the Emperor was abolished, and its independence from the Cabinet was reinforced. While maintaining a close relationship with the Diet, the Board is in charge of reviewing of the public accounts of national administrative agencies and other organizations, and certifying the State's final accounts.