SO2, a pollutant in air, can cause a serious degradation of the proton exchange membrane fuel cell (PEMFC) performance. After direct exposure to 1ppm SO2-air for 50h, the cell voltage degraded by 28%. In order to cope with this problem, an electrochemical filter was fabricated and used for SO2 removal on-board in this study. The modified carbon felt was used as the filter anode. The effect of the applied voltages on the SO2 removal was investigated, and the cell performance was further tested both with and without the filter. When an external voltage of 0.5V was applied across the filter, the cell voltage had no obvious decrease during the 240h test, and cycle voltammery (CV) measurements showed that SO2 was not adsorbed on the cell cathode. The electrochemical filter successfully protected a single cell from being poisoned by 1ppm SO2-air for more than 240h. ► An electrochemical filter is designed and fabricated for the PEMFC application. ► The mechanism of SO2 removal at the filter anode is investigated with linear sweep operations. ► The filter successfully protects a single cell from being poisoned by 1ppm SO2-air for more than 240h.