Over the past decades, container transportation has achieved considerable growth, and maritime trade now constitutes 80% of the global trade. The vessel sizes increased in parallel, up to 21,400 TEU (Twenty-foot-equivalent unit container). Accordingly, global containerized trade reached up to 150 million TEU in 2017 (UNCTAD 2018). This growth brings the need to use scientific methods to manage and operate container terminals more economically throughout the globe. In order to manage container transshipment and to use large vessels efficiently, the docking time at the container port for each vessel should be minimized. The decrease in the docking time enables the vessel to move to its next destination faster, decreasing turnover time and facilitating more containers to be transported. Container terminals can be divided into five main areas as the berth, the quay, the storage yard, the transport area, and the gate. The vessels must be berthed in suitable positions, after which many containers have to be unloaded or loaded via quay cranes, transshipped by vehicles inside the terminal, and stacked by yard cranes to suitable positions, all by using expensive equipment. With the invention of new technologies, the bottleneck at the berth side is almost overcome; however, the yard and the quayside operations have to be further perfected to obtain efficient plans. In this comprehensive literature review study, we aim to combine the literature on both yard and quayside operations, carefully examining independently studied problems as well as integrated ones. General information about port operations and relevant literature is provided. For the quayside, the literature on quay crane assignment and scheduling problems is investigated, whereas, for the yard side, yard crane scheduling, transport vehicle dispatching and scheduling, vehicle routing and traffic control, and storage location and space planning problems are reviewed in depth. In addition to these individual problems, their integrations are also analyzed, relevant publications and their respective contributions are explained in detail. Besides the milestone papers that lead the literature on container terminals, recent publications and advances are also reviewed, and managerial insights and future research directions are identified.