Combined with the success of containerization, globalization has brought about tremendous increases in container transport around the world. Increased container transport leads to larger container ships, which increase demands on seaport container terminals and their equipment. In this situation, the success of container terminals depends on a fast transshipment process combined with reduced costs. It is thus necessary to optimize the three main logistic processes at seaport container terminals: loading and unloading container ships, storing containers, and receiving and delivering containers to and from the hinterland. In another process, the internal transport subsystem ensures the interconnection between previous logistic activities. The optimization of an internal transport cycle is presented for a marine container terminal managed by straddle carriers (SCs), which are among the most used technologies for container transfer. Three subsystems are analyzed in detail: landside transportation, container storage in the yard, and quayside transportation. The conflicts and decisions that arise from operations in these subsystems are analyzed, and optimization algorithms are proposed. Moreover, a simulation is run on Spain's Barcelona Container Terminal to test the algorithms and compare different SC operation strategies (e.g., single cycle versus double cycle) and different-sized fleets of handling equipment. The simulation model is explained in detail, and the main decision-making algorithms from the model are presented and formulated.