The concept of quality is widely used in the practical activity of enterprises. It is necessary to separate the concept of product quality and service quality, since the latter has a number of specific properties that influence the company’s work and its evaluation. The assessment of transport service quality when using railway transport seems to be an urgent task, as this type of mainline transport is of crucial importance for the state. JSC “Russian Railways”, the main railway carrier and infrastructure owner, has a system of premium transport service within the holding structure, which takes on, among other matters, the functions of improving the quality of services provided. A formal approach to transport service simplifies its essence and can lead to wrong decisions in the sphere of management and organisation of work of the transport and logistic company. The article presents the analysis of the transport enterprise performance and an enlarged differentiation of its functions. Moreover, transport service is represented in the form of a pyramid of bases. The quality of each basis should be evaluated and taken into account in the final product of transport service, and this justifies the importance and significance of competent work in all types of activities of transport and logistic enterprise. In addition, logistic principles, the work with human resources, professionalism of managers and many other factors are considered. The study derives a comprehensive quality indicator of the transport and logistic enterprise service, which takes into account all bases of the transport service quality pyramid. The method of Quality Function Deployment is proposed as a method of improving the quality of transport and logistic enterprise services, which allows us to move from the formal assessment of transport service quality indicators to a deep analysis of the activities of the entire enterprise.