The PCARRD Secretariat implements policies and guidelines enunciated by the GC. Its organizational structure is composed of the Office of the Executive Director, the Office of the Deputy Executive Director for Research and Development (ODED-RD) and Office of the Deputy Executive Director for Institution Development and Resource Management (ODED-IDRM), and the PCARRD Directorate or Division Heads.  It is composed of 14 divisions. 

The Executive Director is assisted by the PCARRD Director's Council (DC) which defines R&D priorities and reviews the national R&D program and PCARRD budget  before it recommends  to the Technical Advisory Committee (TAC) or Governing Council (GC). 

Two support divisions, namely, the Planning and Development  as well as Management Information Services directly reports to the Office of the Executive Director (OED).