Nafion® film has been widely used as a representative cationic ion exchange membrane for electrochemical systems including water splitting. However, detailed H+ permeability properties have been poorly understood thus far. We here attempt to relate the H+ permeability with the material properties of Nafion® films. For that, four samples representing two casting types were selected to study the H+ permeability. We conducted the pretreatment to see the effect of the new alignment of the water clusters on the H+ permeability. Although the studied membranes show individual transport features, we observed the increased H+ permeability from 0.05 to 0.5 M concentrations in acidic electrolytes. Such a feature is caused by the increased chemical-potential gradient along with the osmotic de-swelling. We also found that a H+ diffusion channel is associated with the ionic cluster size of the films, which can explain the higher H+ permeability after the pretreatment. Lastly, the individual H+ permeability was obtained when measuring at different electrolytes, revealing that the H+ permeability is strongly influenced by the anionic mobility rather than the acidic dissociation constants. Our results provide a fundamental understanding of the H+ transports through the commercial Nafion® membrane, which gives a guideline for the rational design of ion exchange membranes.