Capacitive deionization (CDI) is an emerging desalination technology with an environmental-friendly operation and energy-efficient properties. However, activated carbon (AC) used for CDI electrode does not have a significant preference toward anions, leading to unnecessary energy consumption for treating fluoridated water. Hence, we achieved selective fluoride removal in CDI system using a reduced graphene oxide/hydroxyapatite composite (rGO/HA), a novel fluoride selective electrode material. The results showed that the rGO/HA electrode has 4.9 times higher fluoride removal capacity than the AC electrode from a ternary solution consisting of fluoride, chloride, and nitrate ions. The fluoride removal capacity increased when the adequate voltage was applied. Furthermore, the rGO/HA electrode exhibited stability and reusability without significant capacity loss even after 50-cycle operation, maintaining about 0.21 mmol g⁻¹ of fluoride removal capacity and approximately 96% of regeneration efficiency. Thus, this study suggests a novel electrode material for effective and selective fluoride removal in the CDI system.