A method for calibrating a fuel control valve assembly including a valve and an actuator is disclosed. The method includes determining an encoder offset by actuating the valve until a predetermined value for the effective flow area is measured to obtain an actual calibration encoder count and comparing the actual calibration encoder count to an initial calibration encoder count. The method also includes adjusting an alignment encoder count and a maximum encoder count by an amount of the encoder offset. The method further includes associating the adjusted alignment encoder count with an alignment command value and the adjusted maximum encoder count with a maximum command value.