The objective of this study is to improve the selective removal of fluoride ions from water using an electrodeposited polyaniline-carbon nanotube (PANI-CNT) composite electrode. The PANI-CNT electrode was successfully fabricated in a partially oxidized emeraldine form, as indicated by the cyclic voltammetry (CV) and X-ray photoelectron spectroscopy (XPS) results. The PANI-CNT composite electrode is dominated by mesopores and presents good hydrophilicity, which improves the mass transfer of ions and ensures better wettability, respectively, during electrochemically controlled separation experiments. The optimal voltage and pH for the fluoride removal are 1.6 V and 7, respectively. The fluoride removal capacity using the PANI-CNT (0.52 mmol g^?1) electrode is larger than that of the carbon nanotube (CNT) (0.34 mmol g^?1) electrode due to the PANI redox reactions. This finding indicates that enhanced fluoride removal from water can be achieved by incorporating PANI with CNTs. More importantly, the selectivity for fluoride over chloride using the PANI-CNT electrode significantly increases from 0.26 to 1.22, suggesting that the composite electrode incorporates fluoride rather than chloride due to the strong electronegativity of fluoride. The PANI-CNT electrode maintains good stability and reversibility for fluoride removal for four electrochemical cycles, which highlights the feasibility of the selective separation of fluoride ions via an electrochemically controlled approach.