This paper addresses the shipment planning problem with random processing times in intermodal logistics via transfer ports. Shipment activities are divided into two groups according to regional settings. Activity processing times in region A are assumed to be random while those in region B are deterministic. At the beginning (stage 1), the forwarder assigns agents to all job activities (planning decision). In case a shipment delay is observed, an in-process adjustment (recourse decision) is implemented (stage 2). A two-stage stochastic programming model is established and an illustrative example is discussed. Managerial insights are presented in a simulation study.