In this article, we describe the use of dynamic simulation when designing an effective system for order picking within a distribution warehouse. The simulation model was created in the Witness software environment for discrete dynamic simulation and is a modification of a general simulation model of material flows in supplier systems. Using the example of a batch system for picking orders in a drugstore goods warehouse, we discuss the possibilities of using a general simulation model of material flows as an effective framework for the development of system support for warehouse processes using WMS. The simulation model is based on the possibility of dividing any material flow in the supply system into a finite number of movements with the possibility of using one of the sources and fulfilment of certain conditions. In order to achieve the required optimisation of the order picking system, which depends, in particular, on the unknown duration of goods collection at the picking location, and on the duration of goods sorting in consolidation, the “what-if” analysis has been used as a tool to measure the impact of uncertainty of one or more variables entering the model on the uncertainty of output variables. The study showed that minimisation of the number of physical elements in the model leads to a significantly higher speed of its operation. By means of dynamic simulation, it is possible to test a large number of variants of the picking system layout in a relatively short time and minimise the risk of erroneous decisions associated with the implementation of a suitable WMS.