Capacitive deionization (CDI) has attracted increasing attention over the past decade for the facile removal of ions from aqueous solutions. Nowadays, CDI is rapidly growing and evolving, and has been applied in many aspects. One important application field is water remediation, i. e., removing ionic contaminants of concern from water. Herein, we investigated the feasibility of perchlorate removal from brackish waters by batch-mode CDI technology. Effects of various operating parameters on dynamic electrosorption processes of both perchlorate and chloride were examined. Meanwhile, a one-dimensional CDI process model for dual-anions was developed to quantitatively describe the electrosorption kinetics of perchlorate and chloride, and an excellent agreement between the modeling results and the experimental data was observed. Experimental results revealed a favorably strong preferential adsorption of ClO4-over Cl-in the studied CDI system under various conditions. Moreover, only slight discrepancy between adsorption-desorption cycles was found, demonstrating the good regeneration of electrodes and operational stability of the CDI cell. Finally, the scale-up studies indicated that the CDI stack with multiple pairs of electrodes could achieve a much more superior ion removal performance than the CDI cell with only one pair of electrodes. To conclude, these results showed that the CDI system was effective for perchlorate selective removal in the presence of other major ions and had potential in treatment of perchloratecontaminated brackish water.