This article presents the results of a numerical investigation, using a comprehensive three-dimensional, single phase, non-isothermal and parallel flow model of a PEM fuel cell with deflected membrane electrode assembly (MEA). This numerical research has concentrated on the deflection parameter (${delta}$) that affects this type of fuel cell performance. The model accounts simultaneously for electrochemical kinetics, current distribution, hydrodynamics, and multicomponent transport. A set of conservation equations valid for flow channels, gas-diffusion electrodes, catalyst layers, and the membrane region are developed and numerically solved using a finite-volume-based computational fluid dynamics technique. Because of importance of base model fuel cell (${delta}$ = 0), initially the CFD result of polarization curve has been validated with the available experimental data which shown good agreement. Introducing of deflection parameter as a criterion for creating of a new geometry, shown that fuel cell performance increases rather than base model, since the face width increases and more reactants diffuse through the gas diffusion layer (GDL) to the reacting area. Also, when this parameter reaches to its maximum value equal to channel height, the fuel cell performance has been maximized in high current densities region. The further numerical results including of temperature distribution, oxygen, and water mass fraction in deflected membrane full cell are derived and discussed in the more details with respect to various values of deflection parameter. Finally, the obtained numerical results shown reasonable features in describing of deflected fuel cell behavior.