Today, green transport is a growing trend in terms of transport costs, CO2 emissions and satisfaction with logistics services. Green logistics is an environmentally friendly and sustainable logistics system that encompasses activities affecting logistics functions and processes, promoting the environment and the development of a circular economy. Rail transport is considered to be one of the least polluting modes of transport, but the fact that only electrified rail represents the concept of green logistics has been underemphasised, as the fleet consisting of diesel trains is a major challenge. This article aims to investigate the implementation of green logistics in railway transport in the case of Lithuania. The scientific literature, SWOT analysis, expert evaluation and parameter correlation methods were used to achieve this goal. An analysis of the internal and external factors of Lithuanian Railways in terms of green logistics has identified the main strengths of rail transport. These are environmental friendliness, electric trains reducing CO2 emissions, a strong focus on circular economy and others. The main weaknesses include the more extensive use of diesel trains, competition, etc. The external factors of the company show that the main opportunities are the reduction in net CO2 emissions to zero, the acquisition of more electric locomotives and others, while the main threats include an increase in energy costs or the complexity of implementing new technologies. An analysis of these factors has led to the construction of a SWOT matrix, which shows that the company’s strategy in the field of green logistics is quite strong, with more strengths than weaknesses. The results made it possible to identify the links between the individual implementation principles of green logistics in railway transport and provide strategic guidelines for the successful integration of green logistic principles into railway transport in Lithuania.