Anionic radionuclides pose one of the highest risks to the long-term safety assessments of disposal repositories. Therefore, techniques to immobilize and separate such anionic radionuclides are of crucial importance from the viewpoints of safety and waste volume reduction. The main objective of this study is to design a separator with minimum pressure disturbance, based on the concept of a conventional cyclone separator. We hypothesize that the anionic radionuclides can be immobilized onto a nanomaterial-based substrate and that the particles generated in the process can flow via water. These particles are denser than water; hence, they can be trapped within the cyclone-type separator because of its design. We conducted particle tracking analysis using computational fluid dynamics (CFD) for the conventional cyclone separator and studied the effects due to the morphology of the separator. The proposed sandglass-like design of the separator shows promising results (i.e., only one out of 10,000 particles escaped to the outlet from the separation zone). To validate the design, we manufactured a laboratory-scale prototype separator and tested it for iron particles; the efficiency was ca. 99%. Furthermore, using an additional magnetic effect with the separator, we could effectively separate particles with ~100% efficiency. The proposed sandglass-like separator can thus be used for effective separation and recovery of immobilized anionic radionuclides.