A microbial fuel cell (MFC) is a bio-electrochemical system that drives a current by mimicking bacterial interactions found in nature. Usually, MFCs use Nafion as a PEM to separate the electrodes while permitting protons transfer between the anode and cathode. However, Nafion is expensive and accounts for a large percentage of the costs in MFC configuration. Here, we show MFCs using hydrocarbon-based PEM, disulfonated poly (arylene ether sulfone) (BPSH), which is considered as one of alternative PEM, and relatively inexpensive as compared with Nafion. BPSH membranes exhibit a comparable performance to Nafion 212. Especially, BPSH 40 and 60 (mole %) have higher proton conductivity than Nafion 212. In a two-chamber system, MFC with BPSH 40 shows higher voltage than that with Nafion 212. MFCs with BPSH 20 and 30 show lower voltage decline than other PEMs. In a single-chamber system, a voltage of MFC with BPSH 40 shows about 30% higher (17 mV) than that with Nafion 212 (13 mV) with internal resistance of 10 Ω. In addition, The MFC with BPSH 40 produced about 10% higher maximum power density (126 mW m −2 ) than that with Nafion 212 (111 mW m −2 ).