The electrochemical properties of a perfluorosulfonic acid (PFSA) membrane are estimated using a combination of molecular dynamics simulation and statistical thermodynamic model. We obtain all parameters in an ionic conductivity model from an atomistic simulation and remove all adjusted model parameters. From a microscopic point of view, the hydrated PFSA membrane shows micro-phase segregation which separated into hydrophilic and hydrophobic phases. Our present work originates with this phenomenon and we treat this phase segregation as if it is a continuous phase for each of which the proton (H+) is transported inside the PFSA membrane/solvent (water and alcohols) mixture. The chemical potential for a given system is estimated using a molecular simulation technique to predict the van der Waals interaction energy between the polymer and solvent. In addition, the self diffusion coefficients are calculated from the molecular dynamics simulation. We study various polymer/solvent compositions to understand the concentration dependence of self diffusion coefficient. Our self diffusion coefficients and also the predicted final ionic conductivity agree well with previously reported experimental data. (C) 2011 Wiley Periodicals, Inc. J Polym Sci Part B: Polym Phys 49: 1455-1463, 2011