Short-lived radioactive metals are important tracers in clinical diagnosis. Radioactive metals for clinical use are produced from suitable target metals in cyclotrons. The trace amount of radioactive metal produced is contained in a relatively large amount of target metal. A rapid and effective method is required to isolate the radioactive metal. In the present study, selective complex formation followed by cation-exchange adsorption was performed in a continuous flow-based system. Ethylenediamine-N,N,N',N'-tetraacetic acid (EDTA) was selected as the ligand after simulation of the separation of radioactive Ga from the target (Zn). Selectively, the Ga-EDTA complex passed through the cation trap, while Zn2+ was trapped. This separation principle is opposite to that of typical solid-phase extraction, which captures the target ion. The proposed separation was performed in a flow-based system with a parallel, open-channel ion trap. The performance was optimized by altering the channel dimensions, channel-filling mesh, and flow rate. Finally, the target radioactive metal, Ga, was selectively and effectively (>99%) separated from a mixture of 50 fg Ga/L and 100 mg Zn/L. The concentration of Zn remaining in the Ga solution was 2.3 μg/L. The complexed Ga was converted to free Ga3+ by a simple UV irradiation method. The proposed method effectively and rapidly separates trace amounts of radioactive metals contained in larger amounts of target metals using a simple flow system that can be operated on site.