The NEDA Regional Office (NRO) XII was first established in Cotabato City pursuant to Presidential Decree No. 742 dated 1 August 1975, restructuring the regional groupings of the provinces in Mindanao, Basilan, Sulu and Tawi-Tawi area. On 25 October 1975, NRO XII became operational with the following divisions to facilitate its operational concerns: the Plan Formulation, Program Coordination and Administrative Division.

The passage of Executive Order (EO) No. 230, “Reorganizing the NEDA”, restructured the NEDA Regional Office divisions to Macro-Intersectoral Coordination and Assistance Division (MICAD), Economic Development Division (EDD), Social Development Division (SDD), Infrastructure Development Division (IDD), and Operations Division (OD).

With the adoption of the functional structure proposed under the NEDA Rationalization Plan per EO No. 366, the divisions were restructured into the Plan and Policy Formulation Division (PPFD), Project Development, Investment Programming and Budgeting Division (PDIPBD), Knowledge Management Division (KMD), Project Monitoring and Evaluation Division (PMED), and the Operations Division (OD).

The approval of the Rationalization Plan of the NEDA pursuant to EO No 366 dated 04 October 2004 renamed the Operations Division to Finance and Administrative Division. With the proposed shift from sectoral to functional compartmentalization in the technical divisions, Plan and Policy Formulation Division was renamed to Policy Formulation and Plan Planning Division and the Knowledge Management Division to Development Research Division to support NROs core operation.  The Project Development, Investment Programming and Budgeting Division and Project Monitoring and Evaluation Division’s name remain the same.