Feedback control systems, of which control loops are closed over a real-time communication network, are called Networked Control Systems (NCSs). Among major problems in Networked Control Systems (NCS) area is providing Quality of Service (QoS) for the underlying communication network. The stability of the NCS strictly depends on the service received from the communication network. The protocol dynamics were not investigated in most of the previous work for the analysis of the performance of the NCS. In this paper, the performance of NCS operating on a FlexRay network is investigated using simulation method considering the effects of the network operation.