Maritime transport in the European Union has increased in the last years, triggering congestion in many of the most important sea and river ports. A lot of works have highlighted how the connection between these ports and dry ports can contribute to reducing port congestion and emission of greenhouse gases (GHGs). This work aims to improve the knowledge about the functionalities of Terminal Operating Systems (TOSs) managing container terminals of sea, river, and dry ports, with the aim of improving their performance and contributing to reducing congestion and GHG emissions to achieve a higher sustainability. The contribution and novelty of this paper in the field of container-terminals logistics research is the use of the Analytic Hierarchy Process (AHP) to identify and hierarchize TOS functionalities. The robustness of the model was checked by applying a sensitivity analysis. One hundred and seven functionalities were grouped into six main clusters: Warehouse, Maritime Operations, Gate, Master Data, Communications, and ERP (Enterprise Resource Planning) Dashboard. The results show that time tracking of vessels, space optimization, development of loading and unloading lists, and optimization of container locations are the most important functionalities of a TOS. This work is addressed to developers, sellers, managers, and users of TOSs and researchers working on container-terminal performance.