The Ministry of Economy is the principal government agency responsible for preparing the national development plans. This ministry started on 24th April 1956 with the establishment of the Economic Secretariat to the Economic Committee of the Federal Executive Council. The Economic Secretariat was reorganized into UPE in 1961 and headed by the Deputy Chief Secretary (Economics) in the Prime Minister's Department. Starting in 1970, the EPU was headed by a Director General with Tan Sri Dato' Thong Yaw Hong appointed as the first Director General.

The Ministry of Economy has gone through several processes of strengthening its functions to strengthen the role of the UPE in planning the country's socioeconomic development. This includes the reorganization of its organizational structure in 2007, which has specialized the field of planning into two sectors, namely macro planning and sectoral planning. In 2009, the Privatization and Financing of Private Initiatives (PFI) Section of the EPU was transferred to the Public Private Cooperation Unit (UKAS), a new agency under the Prime Minister's Department.

With the change of government after the 14th general election in 2018, UPE has been restructured into a ministry, which is the Ministry of Economic Affairs (MEA). MEA's main mandate is to lead the nation's socioeconomic development through quality planning toward inclusive, fair, and equitable national development. In addition, the MEA is also given supervisory responsibility for 31 agencies, statutory bodies, government-related companies and state economic development corporations. Following the decision of the Council of Ministers dated 18 December 2019, the UPE was officially dissolved, with the role and functions of the UPE being taken over by the MEA. With that, the MEA function is more comprehensive, covering aspects of planning, implementation, monitoring, and regulation.

The EPU was re-established as an agency under the Prime Minister's Department following the formation of the new Cabinet on 10 March 2020. The EPU took over the role and responsibilities of the MEA when the MEA was dissolved.

Since its establishment almost six decades ago, the role and function of the EPU in preparing the national development planning plan for the medium and long term have not changed much, even though it has gone through several processes of reorganization, dissolution and re-establishment. EPU always aligns the philosophy of development with changes in Government administration and current development policies.

On 23 December 2022, the EPU was dissolved following a change of government after the 15th general election. The role and responsibilities of the EPU are taken over by the Ministry of Economy, led by the Secretary General, Dato' Nor Azmie bin Diron.