A sulfonated poly(arylene ether sulfone) (SPAES)/polyimide nanofiber (PIN) composite proton exchange membrane was developed for use in microbial electrolysis cells (MECs), where diverse cations that compete with proton coexist in high concentrations. It was fabricated by impregnating SPAES as a proton-conducting polymer into PIN as a supporter for mechanical reinforcement. The membrane showed excellent mechanical and dimensional stability (tensile strength > 40 MPa) due to membrane reinforcement by nanofibers, despite having a high water uptake (35 +/- 3%) and ion exchange capacity (2.3 +/- 0.3 meq/g). This novel membrane was highly selective for protons while excluding other competing cations; thus, it significantly mitigated the proton accumulation problem in the anode when applied to actual MECs. In addition to 1.5-fold greater proton transport, the SPAES/PIN membrane exhibited 3-10-fold less undesirable crossover of other cations depending on the species and 2-2.5-fold less gas permeability compared to Nafion-211 membrane. The application of this membrane improved hydrogen production efficiency of MEC by 32.4% compared to Nafion-211 and better hydrogen purity (90.3% for SPAES/PIN vs. 61.8% for Nafion-211). Therefore, this novel membrane has good potential for MEC applications, especially when protons and other competing cations are present together, due to its superior proton selectivity.