Today’s fast-changing environment for construction companies requires rapid responses and adaptation of their projects. Despite the multitude of tools applied for project cost management in engineering and construction companies, there is a need to form comprehensive solutions. The purpose of the study is to form a methodological approach to project cost management in the field of engineering construction based on alternative models to diagnose the development, assessment and selection of functional areas and content of cost management in the construction project, which allows one to increase adaptability and flexibility in the process of its implementation. The basis of research methodology is modeling, which allows one to adjust the economic and financial flows based on three S-curves, one for each component of the total cost of the work: direct costs, indirect costs and reserves. These curves include the direct cost curve for the main purchasing packages as well. This brings financial flows closer to reality because it is possible to adjust the S-curves according to the behavior of each subsystem. The contribution of the study is the proposed approach of integrating concepts related to the coordination and development of project design and production management (lean construction), forming a “3D model of management”, in a broad and comprehensive management system. It assumes a comprehensive and complete way to manage civil engineering projects. The proposed methodological approach can make a significant contribution to the preparation of forecasts and estimates by planners and controllers in the context of construction projects.