Ultrathin nanoporous (NP) films are an emerging field for selective and effective ion/molecular separation and electrochemical sensing applications. We describe selective ion permeation in surface-functionalized ultrathin NP SiO2 films (NP SiO2-NH2). The ultrathin NP SiO2 films with ca. 8 nm thickness were prepared from silsesquioxane-containing blend polymer Langmuir-Blodgett films (nanosheets) using the photo-oxidation method. The porous SiO2 surface was modified with a pH-responsive amine-containing silane coupling agent. Selective ion permeation was demonstrated under acidic pH conditions (pH ≤ 6) using two equally sized redox probes: negative (Fe(CN)63-/4-) and positive (Ru(NH3)62+/3+) ions. The current density for Fe(CN)63-/4- decreased as the pH value increased to pH = 6, whereas it increased for Ru(NH3)62+/3+. Control measurements revealed that the probes can penetrate the pores of nonfunctionalized SiO2 films irrespective of pH values, indicating that both the size and the surface charge response contributed to selective ion permeation. Results obtained from this study pave the way for new applications in molecular separation and sensing applications based on ultrathin nanoporous films (<10 nm) and tailored surfaces.