Warehouse is a part of logistic system that serves to store products at each node in a supply chain. The presence of specific elements in the fertilizer products causes them not to be stored in any places as it may deteriorate the products. Determining the best scenario in the process of storing fertilizers that have seasonal demand is complex. This is due to the uncertainty in the amount of fertilizer productions at each day, and also the amount of demand orders as well as the arrival time of the delivery orders (DO) for each fertilizer product. In addition, when the warehouses are overcapacity, which is often the case, there is a chance that products are stored outside in the open storage (OPS) or in other warehouses that are not dedicated for the products. Therefore, this paper tries to solve this problem using discrete event simulation method. With this method, different scenarios are possible to be investigated without affecting the daily operational performance. This study aims to provide a recommendation for the scheme of fertilizer storage process in a company so as to reduce the opportunity lost due to product damage.