In this paper, structural analysis is performed to investigate the deformation of porous media in a proton exchange membrane fuel cell (PEMFC). Structural deformation of air plate of the fuel cell causes the change in configuration and cross sectional area of the channel. The distributions of mass flow rate and pressure are major factors to decide the performance of a PEMFC. These factors are affected by channel configuration of air plate. Two kinds of numerical air plate models are suggested for flow analyses. Deformed porous media and undeformed porous media are considered for the two models. The Numerical flow analysis results between deformed porous media and undeformed porous media have some discrepancy in pressure distribution. The pressure and velocity distribution under a working condition are numerically calculated to predict the performance of the air plates. Pressure and velocity distributions are compared for two models. It is shown that structural deformation makes difference in flow analysis results.