EUROCLIO is a non-profit NGO, registered association according to Dutch law. As a member-driven organization it is led by a General Assembly, an elected international board of volunteers (governance experts and history educators) and run by a professional Secretariat. The EUROCLIO board supervises the work of the director, who manages the Secretariat. The Board and Secretariat work together in a Finance-, Membership-, and Policy Committee and meet at least 3 times a year.

The cooperation and division of responsibilities between the board and management is laid down in a management agreement. The roles and responsibilities of the board are set in the statutes and further defined in the internal rules (by-laws). The management at the secretariat has set a well-defined management grid, executes frequent performance reviews and involves staff as much as possible in key decisions, envisioning and contacts with membership.