A method and apparatus for use in controlling the reaction temperature of a fuel processor are disclosed. The apparatus includes a fuel processor reactor, the reactor including a water gas shift reaction section; a temperature sensor disposed within the reaction section; a coolant flow line through the reaction section; and an automated control system. The automated control system controls the reaction temperature by determining a first component for a setting adjustment for the actuator from the measured temperature and a setpoint for the measured temperature; determining a second component for the setting adjustment from a hydrogen production rate for the fuel processor; and determining the setting adjustment from the first and second components.