An ion-exchange method to separate charged biomolecules on ultrathin layer chromatographic (UTLC) plates using electrospun Nafion-Polyacrylonitrile (PAN) nanofibers as the stationary phase is described. Sulfonate groups on Nafion provide the ion-exchange sites. The addition of PAN (a higher molecular weight polymer than Nafion) was used to facilitate the nanofiber formation process using electrospinning. Electrospinning parameters and separation conditions were optimized using fractional factorial design and response surface methodology. Nafion-PAN nanofibers containing 45% (w/w) Nafion with 0.407 mmol/g of SO3H group and 16.0 mmol/g of fluorine as an ion exchange stationary phase for UTLC were evaluated using the separations of amino acids and proteins, followed by visualizations using ninhydrin and fluorescamine, respectively. The electrospun Nafion-PAN plates showed high chemical stability under various mobile phase conditions. Mobile phase velocity decreased with the addition of Nafion into the electrospinning solutions. The sources of band broadening of analyte spots were investigated. The separation of amino acids showed high selectivity and separation efficiency. The separation of four proteins demonstrated the feasibility of Nafion-PAN UTLC for separating large biomolecules. (C) 2017 Elsevier B.V. All rights reserved.