The effects of several electrolyzed waters were evaluated on the permeation of model base, acid and non-ionized compounds, lidocaine (LC), benzoic acid (BA), and isosorbide mononitrate (ISMN), respectively, through excised hairless rat skin. Strong alkaline-electrolyzed reducing water (ERW) enhanced and suppressed the skin permeation of LC and BA, respectively, and it also increased the skin permeation of ISMN, a non-ionized compound. On the contrary, strong acidic electrolyzed oxidizing water (EOW) enhanced BA permeation, whereas suppressing LC permeation. Only a marginal effect was observed on the skin permeation of ISMN by EOW. These marked enhancing effects of ERW on the skin permeation of LC and ISMN were explained by pH partition hypothesis as well as a decrease in skin impedance. The present results strongly support that electrolyzed waters, ERW and EOW, can be used as a new vehicle in topical pharmaceuticals or cosmetics to modify the skin permeation of drugs without severe skin damage.