Nafion- and polybenzimidazole (PBI)-functionalized multiwalled carbon nanotubes (MWCNT–Nafion and MWCNT–PBI) have been prepared through an ozone mediated process and used as additives in the preparation of PBI/MWCNT nanocomposite membranes. Scanning electron microscopy images of the nanocomposite membranes show a high compatibility between functionalized-MWCNTs and the PBI matrix. Addition of the functionalized MWCNTs enhances the thermal and mechanical properties of the composite membranes. Moreover, compared to the proton conductivity of 0.03 S cm−1 of the phosphoric acid (PA)-doped PBI membrane, the PA-doped nanocomposite membranes containing 0.2 wt% of MWCNT–Nafion (N-0.2) and MWCNT–PBI (P-0.2) have proton conductivities of 0.05 and 0.08 S cm−1 at 160 °C under anhydrous conditions, respectively. In single cell tests at 150 °C, N-0.2 and P-0.2 demonstrated maximum power densities of 700 and 600 mW cm−2, respectively. The values are much higher than that found with pristine PBImembrane (530 mW cm−2).