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. 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 automatic ones, an algorithm for smart job allocation and routing of automated vehicles (Straddle Carriers) in terminals is presented in this paper. A management strategy for handling a fleet of autonomous straddle carriers in port yard areas aiming at minimizing the energy consumption while maintaining the performance of the port operations is developed. The strategy is based on a three-layer approach, with job assignment and individual routing at the first two levels and conflict resolution at the last layer, aiming at providing collisionfree trajectories and speed profiles. The algorithm is integrated into the terminal operating system of the port and constitutes a complete solution for small-medium sized ports.