Transportation has an essential place in societies and importance to people in terms of its social and economic aspects. Innovative rail systems need to be integrated with developing technologies for transportation. Systemic failures, personnel errors, sabotage, and cyber-attacks in the techniques used will cause a damaged corporate reputation and revenue losses. In this study, cybersecurity attack methods in smart rail systems were determined, and cyber events occurring worldwide through these technologies were analyzed. Risk analysis in terms of transportation safety in smart rail systems was determined by considering the opinions of 10 different experts along with the Analytic Hierarchical Process (AHP) performance criteria. Informatics experts were selected from a group of people with at least 5–15 years of experience. According to these risk analysis calculations, cybersecurity stood out as the most critical security risk at 27.74%. Other risky areas included physical security, calculated at 14.59%, operator errors at 16.20%, and environmental security at 10.93%.