Over recent years, there has been an increasing interest in automated operations of container terminals throughout Western Europe, starting with ECT in Rotterdam and culminating with Altenwerder in Hamburg. The format for automated container terminal operations is centred on the use of Automated Guided Vehicles for horizontal container movements and Automated Stacking Cranes for vertical movements. To justify the large initial investment required to develop such ports it has to be guaranteed that they will offer a significant operational and performance advantage over alternative setups. With the sheer size and unpredictability of the operations taking place at any time, in order to achieve the needed performance levels movements in the terminal have to be optimally pre‐planned and coordinated, thus resulting to a highly complex optimisation problem. Optimisation methods used in recent automated container terminals operate by decomposing key aspects of the problem into different subproblems, a practice that is known to lead to sub‐optimal solutions in this context. We develop a new control algorithm that jointly optimises most of the problem aspects, based in robust optimisation methods and implement them in prototype terminal control software. Robust optimisation involves the definition of intervals for key parameters, like the start time and duration for individual container movements, and then looks for a solution that minimises maximum regret with respect to particular realisations of parameters. The overall control objective, namely the minimisation of ship loading times, provides the measure of regret. The optimisation takes future events into account through a rolling planning horizon, using intervals to allow for their uncertainty