The continuous development of maritime trade over the last decades has led to a significant growth of needs in every section of maritime transport and port operations. During the next 5 years the annual volume at global container terminals will rise significantly, making terminal utilization rates higher than the ones where the systems operate optimally. Hence, there is a need for finding more efficient, quick and economic ways of transporting, handling and storing goods as well as seeking more productive strategies for yard management and terminal operation. Inspired by markets’ growing demands and the possibilities of transforming conventional vehicles into autonomous ones, an algorithm for smart job allocation and routing of autonomous vehicles (Automated Straddle Carriers) in terminals is presented. A collision-free fleet management algorithm has been developed, aiming at managing fleets and guiding autonomous vehicles in port areas. The algorithm is tested with experimental data to determine the importance of adding a process to avoid collisions.