Nafion has received great attention as a proton conductor that can block negative ions. Here, we report the effect of a Nafion coating on an anodic aluminium oxide (AAO) nanoporous membrane on its function of ion rejection and filtering depending on the electric field. In our experiments, Nafion, once coated, was used to repel the negative ions (anions) from the coated surface, and then selectively allowed positive ions (cations) to pass through the nanopores in the presence of an electric field. To demonstrate the proof-of-concept validation, we coated Nafion solution onto the surface of AAO membranes with 20 nm nanopores average diameter at different solution concentration levels. Vacuum filtration methods for Nafion coating were vertically applied to the plane of an AAO membrane. An electric field was then applied to the upper surface of the Nafion-coated AAO membrane to investigate if ion rejection and filtering was affected by the presence of the electric field. Both anions and cations could pass through the AAO nanopores without an electric field applied. However, only cations could well pass through the AAO nanopores under an electric field, thus effectively blocking anions from passing through the nanopores. This result shows that ion filtration of electrons has been selectively performed while the system also works as a vital catalyst in reactivating Nafion via electrolysis. A saturated viscosity ratio of Nafion solution for the coating was also determined. We believe that this approach is potentially beneficial for better understanding the fundamentals of selective ion filtration in nanostructures and for promoting the use of nanostructures in potential applications such as ion-based water purification and desalination system at the nanoscale in a massively electrically integrated format.