The carbonation effect on alkaline polymer electrolyte fuel cells (APEFCs) was investigated in the present work by the study of single-cell performance and electrochemical AC impedance. The carbonate anions in alkaline polymer electrolyte (APE) were found to lead to a decline in cell performance due to the increase in both the ionic resistance, in comparison to OH − conduction, and the overall reaction resistance. When the OH − in APE was partially or completely replaced with carbonate anions, through exposure to air or immersion in KHCO 3 solution, respectively, the peak power density of H 2 –O 2 APEFC single cell (operated at 60 °C) dropped from 0.61 W/cm 2 to 0.47 and 0.43 W/cm 2 , respectively. When air was used as the oxidant instead of pure O 2 , the performance of APEFC single cell was further reduced because of the lower partial pressure of O 2 ; the peak power density decreased to 0.32 W/cm 2 . If CO 2 was removed from the air, the cell performance increased, to some degree, to 0.41 W/cm 2 . Whereas the influence of deliberate replacement of OH − with carbonate anions in APE is rigid, the carbonation effect caused by air can be alleviated to a large degree by operating the cell under high current density, in which case enormous OH − can be produced to refresh the APE and the electrode surface.