Effective treatment of Cr(VI)-containing wastewater is a great challenge faced by many industries with this situation further complicated by the coexistence of other ions such as Cl−. This study demonstrated the suitability and effectiveness of utilizing flow-electrode capacitive deionization (FCDI) for effective and continuous removal of Cr(VI) from brackish wastewaters. The effects of various influencing factors were systematically investigated, including applied current density, feed concentration of coexisting Cl−, hydraulic residence time (HRT), activated carbon loading, initial solution pH and other common coexisting anions. Results indicated that Cr(VI) was preferentially removed compared to Cl− with a high ion selectivity achievable, and Cr(VI) and Cl− had significantly different removal behaviors in many cases. The steady-state effluent Cl− concentration dropped almost linearly with the increase of current density, while the steady-state effluent Cr(VI) concentration dropped to a value under a small current density and decreased insignificantly in spite of the increase in current density. A larger HRT or activated carbon loading favorably contributed to a lower steady-state effluent concentrations of Cr(VI) and Cl−. Initial pH of feed water around 5–6 without pH adjustment was the most advantageous to the removal of Cr(VI). Different coexisting anions had inhibitory effects on the Cr(VI) removal to varying degrees and the carbonate species was found to have the greatest inhibitory effect. This study is of value in promoting FCDI as a viable technology for treatment of Cr(VI)-containing brackish wastewater.