Battery desalination (BD) is a promising next-generation desalination technology because it is environmentally benign, consumes little energy, and requires only mild operating conditions. However, the BD capacity decreases with long-term operation, which limits its use. Herein, we report a new approach to improve the BD cycling stability by coating battery electrodes with Nafion. Nafion-coated electrodes (NaNiHCF and NaFeHCF) were used with rocking chair desalination, a BD system that pairs two cation-reactive battery electrodes with an anion-exchange membrane. The system maintained 94% retention capacity and approximately 100% Coulombic efficiency after 100 cycles. Moreover, the overall desalination performance was enhanced, achieving high desalination capacity (approx. 72 mg g−1) and lower specific energy consumption (5.6 kJ mole−1). In this study, we describe an effective strategy to improve the overall desalination performance and cycling stability of BD.