Reactor protection system to keep nuclear safety and operational economy of plants requires high reliability. Such a high reliability of the system can be achieved through the redundant design of components. However, common cause failures of components reduce the benefits of redundant design. Thus, the common cause failure analysis, to accurately calculate the reliability of the reactor protection system, is carried out using alpha-factor model. Analysis results to 24 operating months are that 1) the system reliability satisfies the reliability goal of EPRI-URD and 2) the common cause failure contributes 90% of the system unreliability. The uncertainty analysis using alpha factor parameters of 0.05 and 0.95 quantile values shows significantly large difference in the system unreliability.