Water content is one of the critical factors in predicting physical and electrochemical phenomena in Membrane Electrode Assembly(MEA), which is a core element of polymer electrolyte fuel cell(PEFC). Water content directly affects on proton conductivity in MEA and is also a very important parameter in predicting current density distribution. To paraphrase, water content is a critical factor in predicting the performance of PEFC. Therefore, accurate prediction of water content distribution in MEA is important in PEFC modeling. In this paper, in order to directly calculate the water content distribution in MEA, we introduced a mathematical model, which is based on computational fluid dynamics, using internal boundary conditions and validated it by comparing with experimental data.