The chapter aims to discuss the following points: identifying a set of tools which make the operation and management of rail companies more effective; analysing the strategic planning process of rail companies which helps to find a suitable model for adapting the identified tools; selecting the control-based cost and revenue management for a detailed analysis and evaluating models for applying the methodology for the case of rail transport; evaluating a control-based management system model for rail companies; describing the operation processes of the rail controlling information and management system model; making recommendations for the practical adaptation of the evaluated models. The management practices of most railway companies do not yet meet the requirements of market-oriented business organisation. A suitable rail restructuring model involves marketing and innovation policy, as well as a business reorganisation plan. The management of rail companies can be gradually improved by adapting the proposed models and methods.