According to Article 4 and 5 of the Nuclear Safety and Security Commission (NSSC) Notice No. 2020-6, radioactive waste packages should be classified by radioactive levels, and finally permanently shipped to underground or surface disposal facilities. The level of the radioactive waste package is determined based on the concentrations of the radionuclides suggested in Article 8 of NSSC Notice No. 2021-26. Since most of the radionuclides in radioactive wastes are beta nuclides, chemical separation and quantification of the target nuclides are essential. Conventional methods to classify chemically non-volatile radionuclides such as Tc-99, Sr-90, Nb- 94, Fe-55 take a lot of time (about 5 days) and have low efficiency. An automated non-volatile nuclide analysis system based on the continuous chemical separation method of radionuclides has been developed to compensate for this disadvantages of the conventional method in this study. The features of the automated non-volatile nuclide separation system are as follows. First, the amount of secondary waste generated during the chemical separation process is very small. That is, by adopting an open-bed resin column method instead of a closed-bed resin column method, additional fittings and connector are unnecessary during the chemical separation. In addition, because the peristaltic pump is supplied for the sample and solution respectively, it is great effective to prevent cross-contamination between radioactive samples and the acid stock solution for analysis. Second, the factors that may affect results, such as solution amount, operating time and flow rate, are almost constant. By mechanically controlling the flow rate precisely, the operating time and additional factors required during the separation process can be adjusted and predicted in advance, and the uncertainty of the chemical separation process can be significantly reduced. Finally, it is highly usable not only in the continuous separation process but also in the individual separation process. It can be applied to the individual separation process because the user can set the individual sequence using the program. As a result of the performance evaluation of the automation system, recovery rates of about 80–90% and reproducibility within 5% were secured for all of the radionuclides. Furthermore, it was confirmed that the actual work time was reduced by more than 50% compared to the previous manual method. (It was confirmed that the operation time required during the separation process was reduced from 6 days to 3 days.) Based on these results, the automation system is expected to improve the safety of workers in radiation exposure, reduce human error, and improve data reliability.