Systems and methods to control fuel cell stack pressure through a cathode backpressure valve. A flow offset value is used as a capacitance term during transient operational conditions to account for discrepancies between the stack flow setpoint and the actual stack flow. The capacitance term is based on operational parameters, including stack pressure changes, stack coolant temperature and stack volume. The additional flow produced by the capacitance terms may be fed, along with pressure drop models and a valve position model to provide a more accurate prediction of valve position.