A controller is provided for a gas valve including a movable valve element, a main diaphragm chamber having a main diaphragm therein coupled to the valve element to displace the valve element relative to a valve opening, and a servo-regulator diaphragm for regulating flow of gas that acts against the main diaphragm, to adjust the valve element and vary the flow rate. A stepper motor is configured to move in a stepwise manner to displace the servo-regulator diaphragm to adjust the valve element and gas flow rate. The controller for the stepper motor includes a microprocessor that receives an input signal indicating an operating capacity level, and determines the steps the stepper motor must move to displace the servo-regulator diaphragm to establish a flow rate corresponding to the operating capacity level. The microprocessor generates a signal to move the stepper motor the number of steps to adjust the gas valve.