The Secretariat, which was established in September 2008, comprises a mix of full-time and part-time staff. The CEFTA Parties and donors, including the European Commission, currently finance the Secretariat and its activities.

The Secretariat provides an annual report on its activities to the Joint Committee and to the CEFTA Secretariat Steering Committee that includes the CEFTA Parties and all donors that support the activities of the CEFTA Secretariat.