A method of operating a locomotive including a set of electrical traction motors, a fuel cell power module for generating electrical current for the traction motors, an air system for providing an air mass to the fuel cell power module, and a cooling system for cooling the fuel cell power module. When an amount of power is requested from the power module, a required current and a stoic set point for the power module are determined. From the required current, the stoic set point, and numerical factors characterizing the power module, an air mass flow set point is determined for producing the requested amount of power. A compressor set point including speed and torque set points of a compressor motor are determined for the air system to produce the air mass flow corresponding to the requested amount of power.