Reliability and punctuality are the key evaluation criteria in railway service for both passengers and operators. Delays spanning over spatial and temporal dimensions significantly affect the reliability and punctuality level of train operation. The optimization of capacity utilization and timetable design requires the prediction of the reliability and punctuality level of train operations, which is determined by train delays and delay propagation. To predict the punctuality level of train operations, the distributions of arrival and departure delays must be estimated as realistically as possible by taking into account the complex railway network structure and different types of delays caused by route conflict and connected trips. This paper aims to predict the propagation of delays on the railway network in the Greater Sydney area by developing a conditional Bayesian model. In the model, the propagation satisfies the Markov property if one can predict future delay propagation in the network based solely on its present state just as well as one could knowing the process’s full history, so that it is independent of such historical procedures. Meanwhile, we consider the throughput estimation for the cases of delay caused by interchange line conflicts and train connection in this model. To the best of the authors’ knowledge, this is the first work of data-driven delay propagation modeling that examines both spatial and temporal dimensions under four different scenarios for railway networks. Implementation on real-world railway network operation data shows the feasibility and accuracy of the proposed model compared with traditional probability models.