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This paper proposes an efficient way to handle fault in controller area network (CAN)-based networked control system (NCS). A fault in a bus line of CAN will induce a data error which will result in data dropout or time delay, and subsequently may lead to performance degradation or system instability. A strategy to handle fault occurrence in CAN bus is proposed to properly analyze the effect of the fault to CAN-based NCS performance. The fault occurrences are modeled based on fault interarrival time, fault bursts' duration, and Poisson law. Using fault and messages' attributes, response time analysis (RTA) is performed and the probability of control message missing its deadline is calculated. Utilizing the new error handling algorithm to replace the native error handling of CAN, the probability of a control message missing its deadline can be translated into the probability of data dropout for control message. This methodology is evaluated using steer-by-wire system of vehicle to analyze the effect of fault occurrences in CAN. It is found that the proposed error handling mechanism has resulted in better NCS performance and the range of data dropout probability for control message also could be obtained, which serves as crucial input for NCS controller design.