In the present study, multi‐walled carbon nanotubes (MWCNTs) were sulfonated by 1,3‐propane sultone and distillation–precipitation polymerization, respectively, and then incorporated into chitosan (CS) to prepare CS/MWCNTs composite membranes for fuel cell applications. CS/MWCNTs membranes show better thermal and mechanical stability than pure CS membrane due to the strong electrostatic interaction between the SO3H groups of MWCNTs and the NH2 groups of CS, which can restrict the mobility of CS chain. The sulfonated MWCNTs provide efficient proton hopping sites (SO3H, SO3− …. 3+HN), thereby resulting in the formation of continuous proton conducting channels. The composite membranes with 5 wt % of MWCNTs modified by two different ways show a proton conductivity of 0.026 and 0.025 S·cm−1, respectively. In conclusion, CS/MWCNTs membrane is a promising proton exchange membrane for fuel‐cell applications. © 2019 Wiley Periodicals, Inc. J. Appl. Polym. Sci. 2019, 136, 47603.