The selected issues of system engineering methodology in the design of transport systems have been presented. The discussed methodological issues were presented in the example of the metropolitan railway concept project. The system description of the transport project is introduced in accordance with the principles used in systems engineering. The presented case study concerns the methodology of designing the concept of the railway transport system. In the proposed case study, the main issue was the development of a document called the Concept of the Metropolitan Railway System (CoMRS) in the urban area of the Metropolis called in Poland GZM. It was assumed that this document would be a system document developed with the use of Systems Engineering methods in order to build, implement and develop a modern complex railway transport system covering the urban area of the GZM Metropolis. Therefore, in the first place, an additional but essential document was developed – the Methodology for the Metropolitan Railway System Concept (MoCoMRS), which contains a comprehensive methodological description of how to proceed with the use of Systems Engineering methods required for the development of the CoMRS. The methodological guidelines relating to the V model were presented in detail. The methodology description also took into account the system life cycle model in the perspective of the enterprise and systems engineering using the V model. When applying systems engineering in the design of transport systems, it is proposed to use this model, which organizes the system procedure during the design process. The guidelines regarding the use of this model and the application of systems engineering methods for CoMRS, relating, inter alia, to the following design stages: system assumptions, system requirements, high-level design, detailed design, were formulated. The case study of the concept of metropolitan railway presented in this paper is based on a real transport project, and the current stage is working on the preliminary feasibility study of this railway system. It is very important, because it is possible to verify and iteratively correct and update the methodology of designing this railway system depending on the changing conditions and criteria resulting from, among others, different stakeholder aspirations that shape the system requirements. This procedure was also included in the V model in phases of development, construction and implementation of the system, as well as in phases of integration, verification and validation of elements and the entire railway system.