The sustainability of services in undertakings which operate in railway passenger transport is closely connected with efforts to provide high-quality and time-acceptable services to the customer, to achieve lean processes, to standardise work processes, to eliminate wastage and to avoid those activities which do not add any value. Considering its ecological nature and big volume of passenger transport, railway passenger transport represents an irreplaceable sustainable system for the future. These facts and the entry of new railway carriers into this system highlight the importance of managing risks in a progressive way. This article focuses on the options of risk management when versatile and flexible tools, such as Lean tools, are set correctly. The aim of this article is to introduce a proposal for the application and a specific application of Lean philosophy in risk management which impacts train delays in railway passenger transport. From the point of view of quantitative data analysis, multiple mathematical-statistical tests have been used to assess data (e.g., Anderson–Darling test, Kolmogorov–Smirnov test, Jarque–Bera test, two-tailed test, Grubbs’s test and Thompson Tau test). Also, descriptive statistics and ANOVA test (Analysis of Variance) have been applied in the process of evaluating the monitored attributes. In order to assess the data dependency, Chi-Square Test and a correlation analysis have been applied. The research outcomes focus on highlighting the need for a systematic approach for train delays and to avoid delays through risk management. The case study applies selected Lean methods to monitor train delays in selected stations within the main railway corridor of the Slovak Republic for the period from 2015 to 2018. In 2019, the results were processed and created a basis for proposing a unique software tool like an aid for risk management in the case of train delays using Lean philosophy. The flexible software includes the participation of employees, and at the same time, it respects the needs of customers. The research results provide grounds for further study of risks in a challenging environment of railway undertakings, with different types of trains, railway stations as well as entire railway networks. The processed results of the article represent valuable material for railway undertakings not only in Slovakia but also for railway organisations in V4 countries.