A better understanding of turbulent unsteady flows in gas turbine systems is a necessary step toward a breakthrough in compressor applications for hybrid fuel cell gas turbine (FC-GT) systems. In this study, compressor stall/surge analysis for a 220 kW hybrid solid oxide FC-GT system is performed for the two different compressor design configurations of a single-stage and a multi-stage compressor. Control methods have been previously developed at National Fuel Cell Research Center (NFCRC) for this system. These control strategies can prevent the operation of hybrid SOFC-GT near the stall/surge limit line; however, computational fluid dynamics (CFD) tools can provide a better understandig of flow distribution and instabilities near the surge limit of operation. The results show that using a multi-stage compressor is preferred over a single-stage compressor for the 220kW SOFC-GT topping cycle design due to the enhanced ability to sustain flow through the compressor during dynamic operation.