Since the commercial operation of Kori unit 1 in 1978, nuclear power has provided cheap, stable and clean electricity in South-Korea. For decades, the discussion about the spent fuel management has been dominated and the government is responsible for on-going research and development (R&D) related to long-term spent nuclear fuel management. The effective management of spent fuel should be applied from the early stage of the R&D process to licensing phases with the step-by-step evaluation system. As part of follow-up efforts after the Fukushima nuclear accident, the Nuclear Promotion Commission and Nuclear Safety Commission were divided in function as an independent agency for enhancing national nuclear safety and security, which aims to protect the public and environment from undue radiological hazard. The national spent fuel project must have a vibrant program for spent fuel management. Due to the nature of these projects, the establishment of a ‘conformity assessment’ system that collects the opinions from the licensing organisations on the results of research projects from the initial R&D stage should be applied advertently in order to efficiently conduct research projects and enhance public confidence. For the government-led project for spent nuclear fuel management, the adequacy and applicability of its technology R&D as well as its sustainability that includes financial, social and environmental performance measures should be evaluated in each stage. The institutionalisation arrangement, so called ‘conformity assessment system’ for the development of a national spent nuclear fuel management plan and related technology should be developed. This study aims to propose the basic principles for the introduction of the conformity assessment system: (1) national management responsibility, (2) spent fuel management project scope, (3) its management main principles, (4) project implementation system, (5) final management project scope and securing financial resources.