The governing bodies of the Federation of Catholic Universities of Europe and Lebanon are:
- The general assembly composed of all the Presidents and Rectors of the member universities. It meets every year in a different university. It discusses, approves and decides on the main orientations in the following areas: scholarship programs, all academic projects, entry of new members, evolution of statutes, budget, elections (FUCE Board of Directors and representation at IFCU).
- The Board of Directors consists of a President, a Vice-President and six Councilors reflecting the diversity of FUCE members. It meets twice a year and ensures the implementation of the decisions taken at the general assemble. In addition, he is responsible for the good financial administration of the institution.
- The secretariat responsible for the day-to-day management of the FUCE under the responsibility and in close collaboration with the Council and its President.