Despite the keen and continuous interest in the fuel cell system as an alternative electricity generation system, the research has been confined mostly to the electrode material development and stack design. Sometimes, optimal design of the integrated system has also been reported. On the other hand, research on control system design has been scarcely presented even though a fuel cell system may be subject to frequent load change during operation. In this study, a control system structure for a 50kW PAFC (Phosphoric Acid Fuel Cell) system has been presented based on steady state simulation studies using the commercial flow-sheet simulator, HYSYS. The prime difficulty encountered in the fuel cell control system design against load change is that it is not clear which process variable should be regulated in the primary control loop. In this study, through extensive simulation study, the hydrogen utilization ratio has been chosen as a regulation variable for the primary control loop. Since the hydrogen utilization ratio cannot be measured directly, an inference model is devised and proposed, too. On the basis of the concept of the primary control loop, the control structure for the whole PAFC system has been suggested.