Electrochemical ion separation (EIONS) is attracting attention as a new ion separation technology because no by-products are generated during the process. However, conventional EIONS systems have lower selectivity for anions; it has limitations in its application to selective anion extraction. Therefore, it is necessary to develop a new EIONS system with high selectivity for specific anions. In this study, we introduce a highly selective EIONS for Cl- extraction from a mixed solution of Cl- and NO3- using silver/silver-chloride electrodes with a cation exchange membrane. This technique is based on the principle that Ag/AgCl electrodes starts to react with Cl- at a specific potential to remove Cl- from the mixture. As a result, this system removed Cl- with 80 times higher selectivity than its removal of NO3- even at the low cell voltage of 0.3 V. Furthermore, it was found that this system could be operated at a current density as high as 5 mA cm−2, suggesting for rapid extraction. We believe that this system can be feasible for separating Cl- and NO3- electrochemically.