The Japan Arts Council is managed and operated by a staff of about 400 under the leadership of an executive board, which consists of a president, executive directors (three persons), and auditors (two persons).

The Board of Councilors consisting of up to 20 persons of high academic standing authorized by the Ministry of Education, Culture, Sports, Science and Technology, is set up to provide advice and suggestions to the president on important issues concerning the management of the Council. An Evaluation Committee under the Board of Councilors evaluates operations of the Council, and reports results to the Board of Councilors.

Furthermore, the Council consults expert committees such as Japan Arts Fund Management Committee, National Theatre Production Committee, National Theatre Research Projects Committee, National Theatre Successors Training Program Committee and so forth on matters requiring specialized advice and suggestions.
The expert committees are consisted of individuals of high academic standing.