The Republic of Korea (ROK), as a member state of the IAEA, is operating the State’s System of Accounting for and Control (SSAC) and conducting independent national inspections. Furthermore, an evaluation methodology for the material unaccounted for (MUF) is being developed in ROK to enhance capabilities of national inspection. Generally, physical and chemical changes of nuclear material are unavoidable due to the operating system and structure of facilities, an accumulation of material unaccounted for (MUF) has been issued. IAEA developed statistical MUF evaluation method that can be applied to all facilities around the world and it mainly focuses on the diversion detection of nuclear materials in facilities. However, in terms of the national safeguard inspection, an evaluation of accountancy in facilities is additionally needed. Therefore, in this research, a new approach to MUF evaluation is suggested, based on the Guide to the Expression of Uncertainty in Measurement (GUM) that an evaluation of measurement uncertainty factors is straightforward. A hypothetical list of inventory items (LII) which has 6,118 items at the beginning and end of the material balance period, along with 360 inflow and outflow nuclear material items at a virtual fuel fabrication plant was employed for both the conventional IAEA MUF evaluation method and the proposed GUM-based method. To calculate the measurement uncertainty, it was assumed that an electronic balance, gravimetry, and a thermal ionization mass spectrometer were used for a measurement of the mass, concentration, and enrichment of 235U, respectively. Additionally, it was considered that independent and correlated uncertainty factors were defined as random factors and systematic factors for the ease of uncertainty propagation by the GUM. The total MUF uncertainties of IAEA (σMUF) and GUM (uMUF) method were 37.951 and 36.692 kg, respectively, under the aforementioned assumptions. The difference is low, it was demonstrated that the GUM method is applicable to the MUF evaluation. The IAEA method demonstrated its applicability to all nuclear facilities, but its calculated errors exhibited low traceability due to its simplification. In contrast, the calculated uncertainty based on the GUM method exhibited high reliability and traceability, as it allows for individual management of measurement uncertainty based on the facility’s accounting information. Consequently, the application of the GUM approach could offer more benefits than the conventional IAEA method in cases of national safeguard inspections where factor analysis is required for MUF assessment.