The International Secretariat of the World Apostolate of Fatima is a position defined in the Statutes of the organization. It is run by Nuno Prazeres and Ana Reis, under the guidance of the International President. The secretariat is responsible to carry out the policies established by the Board of Trustees in the day to day operation of its affairs, which includes among other things, to keep and maintain the archives of the World Apostolate of Fatima and to maintain a flow of information among the various nations affiliated to the movement. With the Treasure, the Secretariat also administers the budget of the World Apostolate of Fatima.

As an international organization involving many cultures it is important that the message and functioning of the organization is uniform throughout the world. The secretariat performs a critical role in this, by assisting the various countries in their formation and growth, insuring that each nation is acting in a manner which is consistent with the statutes and that the Message of Fatima is not corrupted.