In this study, the two-chambered microbial fuel cell (MFC) was continuously long-term operated a young landfill leachate in order to evaluate the impact of cation exchange membrane (CEM) fouling on MFC performance. During the operation, the voltage output decreased sharply to almost zero and the voltage output was recovered completely after replacement of CEM, which implied that the voltage decrease was totally due to fouling of the CEM with the observations of attenuated total reflection Fourier transform infrared (ATR-FTIR) spectroscopy, the scanning electron microscopy (SEM) and long-term operation. The fouled membrane was washed with H2SO4 in order to recover the CEM via removing salts on membrane surface and the replacement of cations on the negatively charged sufonate sulfonate groups with the H+. After acid treatment, the current and power recoveries were only around 38% and 15%, respectively. The membrane was completely fouled again after one week of operation. Moreover, an alkali treatment with NaOH was applied in order to recover the CEM by removing organics on membrane surface. However, the alkali treatment had almost no effect on the fouled membrane depending on current output.