This paper presents a dynamic nonlinear model for polymer electrolyte membrane fuel cells (PEMFCs). A nonlinear controller is designed based on the proposed model to prolong the stack life of the PEM fuel cells. Since it is known that large deviations between hydrogen and oxygen partial pressures can cause severe membrane damage in the fuel cell, feedback linearization is applied to the PEM fuel cell system so that the deviation can be kept as small as possible during disturbances or load variations. A dynamic PEM fuel cell model is proposed as a nonlinear, multiple-input multiple-output system so that feedback linearization can be directly utilized. During the control design, hydrogen and oxygen inlet flow rates are defined as the control variables, and the pressures of hydrogen and oxygen are appropriately defined as the control objectives. The details of the design of the control scheme are provided in the paper. The proposed dynamic model was tested by comparing the simulation results with the experimental data previously published. The simulation results show that PEMFCs equipped with the proposed nonlinear controls have better transient performances than those with linear controls.