A novel double layer proton exchange membrane (PEM) comprising a layer of structurally modified chitosan, as a methanol barrier layer, coated on Nafion (R) 112 was prepared and assessed for direct methanol fuel cell (DMFC) applications. Scanning electron microscope (SEM) micrographs of the designed membrane revealed a tight adherence between layers, which indicate the high affinity of opposite charged polyelectrolyte layers. Proton conductivity and methanol permeability measurements showed improved transport properties of the designed membrane compared to Nafion (R) 117. Moreover, DMFC performance tests revealed a higher open circuit voltage and power density, as well as overall fuel cell efficiency for the double layer membrane in comparison with Nafion (R) 117, especially at elevated methanol solution feed. The obtained results indicate the designed double layer membrane as a promising PEM for high-performance DMFC applications.