The workloads at seaport container terminals are increasing; thus, to enhance performance, the focus on improving container stacking is argued to be an integral factor that should be studied. The main problem is the number of unproductive moves of handling containers. A well-planned stacking area is argued to be a key requirement in order to increase the performance of the terminal operations and assist in maximum utilization of existing resources. In this work, we investigated and then propose the best possible solution by evaluating GAs in order to minimize the unproductive moves often witnessed in terminal operations. A discrete-event simulation CSS model has been developed to study the inbound container stacking that considers in the model the following: the working of the yard crane, Automated Guided Vehicles, delivery trucks and obtain the simulation-based results of GA. We propose a mathematical model to minimize the container handling costs during stacking and retrieval operations in the container terminal yard.