Performance degradation caused by the oxidation of carbon anodes during capacitive deionization (CDI) remains a major problem that may greatly restrict the practical application of CDI. To improve the cyclic stability of CDI, carbon-based anode materials were replaced by pseudocapacitive MnO2 in this work. The cation-selective MnO2 anode was assembled with an anion-selective quaternized poly(4-vinylpyridine)-coated activated carbon cathode into a hybrid CDI cell. The cell exhibited inverted CDI performance with a wide operating voltage window of 1.4 V and a salt adsorption capacity (SAC) of 14.9 mg/g in 500 mg/L NaCl. The SAC retention ratio of the cell can be as high as 95.4% after 350 adsorption–desorption cycles at 1.0/0 V, while that of the CDI cell consisting of activated carbon electrodes was only 15.7% after 285 cycles. The enhanced cyclic stability of the hybrid CDI cell is attributed to the employment of the MnO2 anode, which avoided the use and oxidation of carbon anodes.