The Board of Trustees is the representative decision-making and executive organ of the Council. It contributes to the development and progress of member universities through research and surveys, autonomous consultations on common issues, and recommendations to the government.

The Board is composed of a chairman, three vice-chairmen, between ten and twenty trustees, and two auditors elected from among the presidents of member universities by the General Assembly and approved by the Minister of Education. The KCUE Secretary-General is a trustee ex officio. Trustees are nominated with consideration given to rotating membership among member universities, regions, institutional specializations, membership on KCUE committees, etc.

The functions of the Board of Trustees include planning and directing KCUE affairs, executing tasks related to Council affairs, managing budgets and accounts, carrying out duties mandated by the General Assembly, and performing other duties important to Council operations. The Board meets bimonthly, and decisions are made by majority agreement.