The preparation and characterization of the nanocomposite polyelectrolyte membranes, based on Nafion, sulfonated multi‐walled carbon nanotubes (MWCNT‐SO3H) and imidazole modified multi‐walled carbon nanotubes (MWCNT‐Im), for direct methanol fuel cell applications is described. The results showed that the modification of multi‐walled carbon nanotubes (MWCNT) with proton‐conducting groups (sulfonic acid groups or imidazole groups) could enhance the proton conductivity of the nanocomposite membranes in comparison to Nafion 117. Regarding the interactions between the protonated imidazole groups, grafted on the surface of MWCNT, and the negatively charged sulfonic acid groups of Nafion, new electrostatic interactions can be formed in the interface of the Nafion and MWCNT‐Im, which result in both lower methanol permeability and higher proton conductivity. The physical characteristics of these manufactured nanocomposite membranes were investigated by thermogravimetric analysis, differential scanning calorimetry, Fourier transform infrared spectroscopy, water uptake, methanol permeability, and ion exchange capacity, as well as proton conductivity. The Nafion/MWCNT‐Im membranes showed the higher proton conductivity, lower methanol permeability, and, as a consequence, a higher selectivity parameter in comparison to the neat Nafion or Nafion membrane containing MWCNT‐SO3H or ─OH functionalized multi‐walled carbon nanotubes (MWCNT‐OH) membranes. The obtained results indicated that the Nafion/MWCNT‐Im membranes could be used as efficient polyelectrolyte membranes for direct methanol fuel cell applications.