In highly dynamic and uncertain transport conditions, transport transit time has to be continuously monitored so that the service level is ensured at a proper cost. The aim of this research is to propose and to test a procedure which allows an agile planning and control of transport flows in port logistic systems. The procedure couples an agent-based simulation and a queueing theory model. In this paper, the transport scheduling performed by an agent at the intermodal terminal was taken into consideration. The decision-making agent takes into account data which is acquired in remote points of the system. The obtained results indicate the relevance of continuously considering, for the transport planning and control, the expected transit time and further waiting times along port logistic systems.