Modern rail–rail transshipment yards serve as hub nodes in railway networks and enable a rapid consolidation of containers among freight trains. The container transshipment is executed by parallel gantry cranes supported by a sorting system, where shuttle cars preposition containers to relieve the cranes from excessive movement along the spread of the yard. An important decision problem in this context is the scheduling of the gantry cranes, which is considerably complicated by the need to synchronize cranes and shuttle cars whenever container moves are executed via the sorting system. We formalize the resulting interdependent crane and shuttle car scheduling problem, introduce suited solution algorithms, and apply them in order to explore important managerial aspects. Our main findings in this regard are that the position of the sorter either in the middle of the tracks or at the outside has negligible impact on yard performance, while it is a challenging task to match the number of cranes with an appropriate fleet size of shuttles.