With South Korea increasingly focusing on nuclear energy, the management of spent nuclear fuel has attracted considerable attention in South Korea. This study established a novel procedure for selecting safety-relevant radionuclides for long-term safety assessments of a deep geological repository in South Korea. Statistical evaluations were performed to identify the design basis reference spent nuclear fuels and evaluate the source term for up to one million years. Safety-relevant radionuclides were determined based on the half-life criteria, the projected activities for the design basis reference spent nuclear fuel, and the annual limit of ingestion set by the Nuclear Safety and Security Commission Notification No. 2019-10 without considering their chemical and hydrogeological properties. The proposed process was used to select 56 radionuclides, comprising 27 fission and activation products and 29 actinide nuclides. This study explains first the determination of the design basis reference spent nuclear fuels, followed by a comprehensive discussion on the selection criteria and methodology for safety-relevant radionuclides.