Selective capacitive deionization (SCDI) is a promising desalination process for preferentially removing specific ions from waters with complex compositions. Its selectivity towards certain species can be achieved through novel electrode materials with high affinities towards targeted ions. In this work, we studied the selective removal of fluoride ions from groundwater containing concentrated co-existing chloride ions. A carbon nanotube-CeO2 (CNT-CeO2) electrode was employed for electro-sorption of fluoride ions. When processing a F−/Cl− mixed solution containing 10 mg/L F− and 100 mg/L Cl−, the CNT-CeO2 electrode reduced the concentration of F− ions to 1.5 mg/L in 150 min, amounting to a 85% F− removal efficiency, while Cl− removal was below 2%. This corresponds to a separation factor of 4.16, which is 40x higher than that of conventional AC electrodes. The high affinity of CNT-CeO2 to fluoride could be attributed to the entrance of fluoride ions into the crystal lattice of the CeO2 and the subsequent substitution for lattice oxygen atoms. The addition of CNTs offers substantial improvements in conductivity of the electrode and restricts the aggregation of CeO2, accelerating ion diffusion and selective adsorption. In addition, a selective CDI adsorption-desorption transport model was developed to describe the defluoridation process.