The General Assembly is the highest decision-making organ of the Council and is composed of the presidents or delegated representatives of most four-year higher education institutions in Korea. The General Assembly elects members of the Board of Trustees, amends the KCUE articles of association, approves budgets and account settlements, approves project proposals, and performs other duties critical to Council operations.

Regular sessions of the General Assembly are held annually, and special sessions are convened at the discretion of the chairman of the Board of Trustees. One special session is held each year at the annual Summer Seminar for University Presidents to provide training opportunities. General Assembly sessions are attended by university presidents or other university officials designated by the president. Discussions on key issues common to member universities, such as those related to academic affairs, finances, and facilities, are held during these sessions. The minister of education of Korea also attends all sessions of the General Assembly to elucidate government policy directions.