Load following fuel cell systems depend on control of reactant flow and regulation of DC bus voltage during load (current) drawn from them. To this end, we model and analyse the dynamics of a fuel cell system equipped with a compressor and a DC-DC converter. We then employ model-based control techniques to tune two separate controllers for the compressor and the converter. We demonstrate that the lack of communication and co-ordination between the two controllers entails a severe tradeoff in achieving the stack and power output objectives. A co-ordinated controller is finally designed that manages the air and the electron flow control in an optimal way, We demonstrate our results during specific and critical load changes around a nominal operating point. Although our analysis does not cover wide operating region, it provides insight on the level of controller co-ordination necessary in non-hybridized fuel cell power supply. The shut-down and start-up procedures will be investigated in future work. Copyright (c) 2005 John Wiley & Sons, Ltd.