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Honeywell Engines and Systems (E&S) Environmental Control Systems (ECS) division has been developing a 50 kW proton exchange membrane (PEM) fuel cell brassboard system for automotive application as part of a U.S. Department of Energy (DOE) program. A primary issue in the development of the brassboard is the automatic control of the system. A preferred DOE requirement is dynamic load following from idle to peak power. Since the PEM stacks require precise inlet condition control for both the air and fuel to achieve high efficiency, the control system must provide good dynamic tracking and low steady-state error over the entire operating range. In addition, the controller must provide automatic system start-up and shutdown, built-in-test (BIT) to monitor key system parameters, and take corrective action if those parameters reach an unsafe condition. The purpose of this paper is to present the control system design approach taken by the authors to achieve those goals.