FLAR has an administrative committee, a technical committee, and an executive director.

Administrative Committee: the main organ of FLAR, formed by one representative and a substitute from each country with an equal voice and vote.

Technical Committee: in charge of establishing research guidelines and priorities to develop research, as well as coordinating and evaluating current and ongoing projects.

Executive Director: The Executive Director is elected and evaluated by the Administrative Committee, serves as a link and representative of the Fund, and coordinates and controls FLAR's technical and administrative activities. As well as this the director works to implement FLAR’s strategies and to achieve its goals. Gonzalo Zorrilla de San Martín has been the Executive Director of FLAR since November 2005. His predecessor was Luis Roberto Sanint, who was director for 10 years (1995-2005).