Kansai Christian School operates as a Japanese Zaidan Hojin. The Board of Regents provides general oversight for the school with its members being selected from among Christians with a long-standing commitment to, and understanding of the school, Christian education, and the school's Japanese context. 

The Board of Operations provides more detailed oversight and decision making and consists of members of the school's founding missions, community members, and other key members of the school community. Missions represented on the Board of Operations are North American Baptist, Christian Churches/Churches of Christ, and Bethany International.

KCS is a member school of the Association of Christian Schools International (ACSI).