In recent years, rapid and significant advances in fuel cell technology, together with advances in power electronics and control methodology, has enabled the development of high performance fuel cell powered electric vehicles. A key advance is that the low temperature (80°C) proton-exchange-membrane (PEM) fuel cell has become mature and robust enough to be used for automotive applications. Apart from the apparent advantage of lower vehicle emission, the overall fuel cell vehicle static and dynamic performance and power and energy efficiency are critically dependent on the intelligent design of the control systems and control methodologies. These include the control of: fuel cell heat and water management, fuel (hydrogen) and air (oxygen) supply and distribution, electric drive, main and auxiliary power management, and overall powertrain and vehicle systems. In the case of using an on-board fuel processor as the hydrogen supply system, the control challenges become more extensive and difficult requiring innovative management of slower heat transfer and chemical reaction effects for cold start-up and turn-down transient operations as well as the control of the mass flow, pressure and temperature of the fuel, water and air supply. This paper describes the variety of control challenges being encountered and the methodologies being used for the successful development of affordable fuel cell vehicles.