In this study, transient responses of a polymer electrolyte fuel cell system were performed to understand the effect of sensor fault signal on the temperature sensor of the stack and the coolant inlet. We designed a system-level fuel cell model including a thermal management system, and a controller to analyze the dynamic behavior of fuel cell system applied with variable sensor fault scenarios such as stuck, offset, and scaling. Under drastic load variations, transient behavior is affected by fault signals of the sensor. Especially, the net power of the faulty system is 45.9 kW. On the other hand, the net power of the fault free system is 46.1 kW. Therefore, the net power of a faulty system is about 0.2 kW lower than that of a fault-free system. This analysis can help in understanding the transient behavior of fuel cell systems at the system level under fault situations and provide a proper failure avoidance control strategy for the fuel cell system.