In a polymer electrolyte fuel cell (PEFC), water generation, electroosmosis drag, and back diffusion change the humidity, which affects transport properties such as proton conductivity, effective oxygen diffusion coefficient, and permeance of the feed gas through a membrane. Since the sorption and desorption of water in the electrolyte membrane is slower than other processes such as the oxygen reduction reaction, the proton transport, and the oxygen diffusion, dynamic water behavior should be considered to estimate the cell performance precisely. In this study, the water permeation flux through a membrane electrode assembly (MEA) was measured, and the effective water diffusion coefficients in a membrane and catalyst layer (CL) were formulated as a function of temperature and the moisture content respectively. Dynamic moisture content change in MEA was simulated with the measured effective diffusion coefficients. The experimental results showed that desorption was slower than sorption in the identical moisture content range particularly at the beginning, and this tendency was successfully reproduced using the moisture content distribution obtained by numerical simulation.