A systems perspective for regional strategic transportation planning (RSTP) for freight movements involves an understanding of Supply Chain Management (SCM). This paper starts from the premise that the public sector needs to enhance economic development in the form of providing and ensuring the operation of sufficient network capacity for freight needs but at the same time secure the region’s long term environmental and societal well being. The need for long-term integrated transportation planning that is sensitive to supply chain needs and environmental nuances can be supported by the use of engineering systems methodologies. Here we demonstrate the use and potential of three such methods: Design Structure Matrix (DSM), System Architecture (SA) and System Dynamics in support of a transportation planning process that integrates SCM considerations into RSTP.