This research paper focuses on improving the performance of cross-docking operations under uncertainty in the context of e-commerce logistics. The growth of e-commerce sales has increased product returns and complexity to supply chains. To address this issue, this study investigates how cross-docking operations can be improved under external and internal uncertainty factors. The research begins with a literature review to understand cross-docking facilities (CDFs) and measures to mitigate the effects of uncertainty. The current state of a CDF in a case study for a Fourth Party Logistics (4PL) provider is examined, and by reflecting on the literature overview, two potential means for decreasing the effects of uncertainty are identified: staging-level design and load carrier-type design. A Discrete Event Simulation (DES) model is developed to test the effects of staging-level design and load carrier types on the performance of the CDF. The simulation model captures input factors such as truck arrivals, freight levels, and the purity level of cross-docking. The simulation model’s performance is tested for different scenarios, and the effects of different design alternatives are analyzed. The results demonstrate that two-stage cross-docking with pallets can significantly reduce the total makespan and improve operational efficiency compared to single-stage cross-docking with pallets. The results also show that using roll containers significantly decreases the chance of intra-terminal congestion but also results in longer unloading and reloading times. The research contributes to the understanding of cross-docking operations under uncertainty, stresses the importance of staginglevel and load carrier type design on CDF performance, and provides insights for logistics companies seeking to optimize their e-commerce supply chains.