To analyze the physical phenomena occurring in the Proton Exchange Membrane Fuel Cell (PEMFC) using Computational Fluid Dynamics (CFD) technique under an isothermal operating condition, four major governing equations such as continuity equation, momentum conservation equation, species transport equation and charge conservation equation should be solved. Among these governing equations, using the interfacial boundary condition is necessary for solving the water transport equation properly since the concept of water concentration in membrane/electrode assembly (MEA) and other regions is totally different. It was first attempted to solve the water transport equation directly in the MEA region by using interfacial boundary condition; and physically-meaningful data such as water content, proton conductivity, etc. were successfully obtained. A detailed problem-solving methodology for PEMFC is presented and result comparison with experimental data is also implemented in this paper.