Carbon nanotubes functionalized with proton acceptor groups are obtained for their use as dopants for hybrid materials based on an MF-4SC perfluorinated sulfonated membrane. Ion conductivity at high and low relative humidity, diffusion permeability of hydrochloric acid and methanol permeability, interdiffusion of H+/Na+ ions and mechanical properties of the final hybrid materials are studied as well. Introducing a small amount of dopant (0.5 wt %) is shown to favor an increase in ion conductivity at both high and low humidity, along with a decrease in methanol permeability, compared to the analogous initial membrane. In the specimens with 1–3 wt % of dopant, cation transport selectivity is higher than in the initial MF-4SC membrane. Furthermore, the mechanical properties of hybrid materials are found to not deteriorate, at least.