Disclosed is a system and method for controlling a fuel cell system. More specifically, a fuel cell demand current is calculated based on a driver demand current calculated from a driver demand torque. Then a target flow rate-1 of air to be supplied to a fuel cell stack is calculated based on the fuel cell demand current and a target stoichiometric ratio (SR) of air. The target flow rate-1 is then compensated for using the target SR, an RPM command value of an air blower is calculated based on a compensated target flow rate-2 and the amount of air currently measured. The operation of the air blower is subsequently controlled based on the calculated RPM command value.