Abstract The pH dependence of amino acid transport through a cation exchange membrane (Nafion® membrane) was investigated in the presence of an electric field. The amino acids used in this study are alanine, aspartic acid, phenylalanine, and lysine. Ionic fractions of amino acid at a given pH were calculated and used to derive the average molecular charge of amino acid. The average charge vs. pH is useful in selecting the operation pH at which transport efficiency and separation of amino acids are enhanced. A higher transport rate is obtained at a pH where the positively charged form is dominant. The noncharged form of amino acid can also be transported through a Nafion membrane. Transport rate of the negatively charged species is negligible. A prediction method for electrokinetic transport rate was developed. The method requires values of the diffusivity and mobility of individual ionic form. The values were determined experimentally at a pH where only one ionic form was dominant.