The Agency is managed by a Director who organizes and manages the operations, independently makes decisions within the scope of his competence, represents the Agency before third parties and is responsible for the legality of the operations.

The Director of the Agency has a Deputy.

The Director and the Deputy Director are appointed and dismissed by the Government of Republic of Macedonia at the proposal by the Minister of Labor and Social Policy. The term of office is four years, with the possibility of re-election.