A fuel cell system in accordance with the invention includes a single, central electronic controller (CPU) for controlling at least the Air Handling sub-system, the Reformer sub-system, the Power Electronics sub-system, and the Customer Interface sub-system. The central controller provides a central location for easier serviceability; increases data transport efficiency by eliminating lengthy links between distributed controllers; eliminates the need for multiple mechanical enclosures; allows for controller thermo conditioning in one mechanical enclosure; and reduces parasitic power losses by employing a single power supply.