Polymer electrolyte membrane fuel cell performance has been enhanced with efficient water management by modification of the structure of the catalyst layer. Polytetrafluoroethylene (PTFE) was added to the catalyst layer structure by using two-step catalyst ink preparation method. Physical and electrochemical characterization of catalyst layers with hydrophobic nanoparticles were investigated via TGA-DTA, XRD, nitrogen physisorption, SEM, TEM, EDX analysis, and cyclic voltammetry technique. In addition, performance tests of MEAs were carried out. Catalyst layer structure after performance tests was observed by SEM analysis. Tubular open-ended mesopores have been constructed through the catalysts with hydrophobic nanoparticle addition. PTFE addition to the catalyst layer structure decreased both electrochemical surface area and Pt utilization. Mesoporous hydrophobic channels in the catalyst layer provided decreasing mass transport limitations at higher current densities, by this way, power density of Pt/C-Nafion/PTFE catalyst enhanced. It is concluded that mesoporous hydrophobic channels through the catalyst layer facilitate water removal. Copyright (c) 2015, Hydrogen Energy Publications, LLC. Published by Elsevier Ltd. All rights reserved.