The CYTED Programme is organized according to a decentralized model, whose institutional framework is comprised of the ONCYT, the bodies responsible for the scientific and technological policies of the 21 participating countries. Each ONCYT is responsible for the management of the Programme in their country and participates with a representative in the administration bodies of CYTED.
The General Assembly is the highest level political decision-making body of the CYTED Programme. It is integrated by the highest authorities of the ONCYT.

The General Secretariat is the management body of the CYTED Programme, and which is of international nature. It is directed by the Secretary General, who is appointed every 3 years by the General Assembly and is in charge of carrying out the delineated management guidelines. The General Secretariat includes the technical management bodies of CYTED, which are the Area Committees, each headed by a manager expert in each area of ​​interest of the Programme. The Area Managers are appointed by the General Assembly for a period of two years and may be elected for a further period. It also includes the Scientific Coordinator and the technical staff that provides support in the secretariat at the headquarters located in Madrid (Spain).