A system and method for operating a mass flow controller is described. One embodiment validates the operation of a mass flow controller thermal sensor, including detecting zero drift and span drift in the sensor by comparing the thermal sensor output to a pressure sensor output. In one embodiment, each sensor provides a signal to a digital controller or other processing unit and the controller calculates the mass flow rates of a gas flowing through the unit as measured by the sensors. The mass flow rates may then be compared to determine if one of the thermal sensor is operating properly.