Successful flow-shop scheduling outlines a more rapid and efficient process of order fulfilment in warehouse activities. Indeed the way and the speed of order processing and, in particular, the operations concerning materials handling between the upper stocking area and a lower forward picking one must be optimized. The two activities, drops and pickings, have considerable impact on important performance parameters for Supply Chain wholesaler companies. In this paper, a new flow shop scheduling algorithm is formulated in order to process a greater number of orders by replacing the FIFO logic for the drops activities of a wholesaler company on a daily basis. The System Dynamics modelling and simulation have been used to simulate the actual scenario and the output solutions. Finally, a t-Student test validates the modelled algorithm, granting that it can be used for all wholesalers based on drop and picking activities.