Air and rail transportation systems are characterized by important common features: they serve a significant share of passenger traffic in Europe; their functioning relies on the cooperation of many stakeholders operating a fixed timetable, often with competing objectives; and they have been characterized by quite a fragmented development following national borders. For these systems, the European Commission envisages a common future in terms of an increase of efficiency and elimination of national borders. In this paper, we analyze the two systems in the perspective of their common development and we underline the main existing differences linked to the management of the infrastructure. These differences concern the processes implemented for specifying and allocating capacity, both in strategic planning and in real-time intervention. Our analysis suggests that the air transportation system is moving in the direction indicated by the European Commission, as well as the rail transportation system for what concerns international train paths (typically high-speed trains). However, a substantial separation still exists between conventional rail transportation systems of different countries.