Multi-walled carbon nanotube (MWCNT)/MnO2 supercapacitor electrodes containing MnO2 nanoflakes in the MWCNT network are fabricated through the oxidation of manganese acetate with poly(4-styrenesulfonic acid) (PSS) dispersed MWCNTs. The structural evolution of the electrodes under charge/discharge (reduction/oxidation) cycles and its impact on the electrodes’ electrochemical properties are evaluated. Structural evolution involves the dissolution of MnO2 upon reduction, the diffusion of the reduced Mn species from the MWCNT network toward the electrolyte solution, and the deposition of MnO2 on the electrode surface upon oxidation. Electrode structural changes, including the electrode dissolution and the growth of the MnO2 crystals, are scan rate dependent and have deteriorating effect on the electrode's electrochemical properties including the specific capacitance and cyclic stability.