In this paper, nonlinear and bilinear dynamic models are derived that include the dominant dynamics of the air pressure and flow in a fuel cell system. A two-degree-of-freedom sliding mode control system is also designed using a linear time-invariant state-space model derived from the nonlinear model. A precompensator is also designed that takes into account exhaust gas flow passing through the throttle valve. The precompensator shapes the pressure and flow references and makes the exhaust gas flow passing through the throttle during transient response approximate the desired flow. The precompensator also makes the references approximate static references for appropriately operating the fuel cell system in a static state. This paper presents the architecture of the precompensator, which takes into account the tracking performance for the static references and flow passing through the throttle in a transient state. Numerical calculations and experimental results are presented to verify that the nonlinear model accurately simulates the transient responses of the actual system and that the proposed techniques improve the transient pressure and flow responses in the fuel cell system.