A system for controlling the power output of a fuel cell stack and a battery in a hybrid fuel cell system. The system includes a power damping filter that receives a power request signal, and damps the request to reduce large changes in the power request. A battery state of charge controller receives the difference between a battery state of charge set-point and the actual battery state of charge, and provides a battery power signal that attempts to maintain the battery state of charge at the set-point. The damped power signal and the battery power signal are added to generate a system power demand signal that satisfies the driver power request using the battery power and fuel cell stack power, and uses the fuel cell stack power to charge the battery during low power transients or if the battery state of charge is below the set-point.