The Board of the Fund is appointed jointly by the British and Irish Governments. It is assisted by an Advisory Committee comprised of senior officials appointed by the two Governments.

The administration of the Fund is provided by a Secretariat, headed by Joint Directors General based in Belfast and Dublin. A range of bodies act as managing agents for the Fund and there is also a team of Development Officers, located across the southern border counties, who act as local contact points for the Fund and assist prospective applicants in identifying and developing proposals. They also monitor the ongoing operation of projects, providing support and financial assistance as necessary.

The United States of America, the European Union, Canada, Australia and New Zealand are represented by their international observers at meetings of the Board.