The article presents modern international approaches to public participation in Sustainable Transport System planning. It discusses the causes of social conflicts during the implementation of transport infrastructure projects using the example of implementation of several Polish strategic road infrastructure projects. It provides the assessment of the form, scope, and scale of stakeholders’ involvement in the decision-making process. Among mitigation measures, the authors propose a model solution based on a comprehensive approach to public participation in road infrastructure planning in smart cities and smart villages within a Sustainable Transport System. The proposed idea involves a model of multi-criteria spatial analysis using the analytic hierarchy process (AHP) developed in the geographical information systems (GIS) environment, which—apart from technical-functional, environmental, cultural, economic, financial, and social criteria—also encompasses preferences expressed by local community representatives. The model includes eight stages of public participation in the decision-making process, involving all the rungs of a ladder of citizen participation. The presented solution departs from typical social participation methods used in road infrastructure planning processes.