Due to the highly competitive modern business environment, manufacturers must be flexible in order to provide customized and high quality products within a short period of time. The warehouse operations of manufacturers have become complex and uncertain due to the offering of various customized products to fulfil customer needs. With limited time and resources, it is a challenge for manufacturers to manage the warehouse workflow in an effective way so as to maintain customer satisfaction and services quality. Moreover, possible risks that may occur during warehouse operations can have negative impacts on the performance of manufacturers. In this paper, a Workflow Decision Support System (WDSS) is proposed to formulate the warehouse operations workflow with consideration of risk management concepts. Radio Frequency Identification (RFID) is adopted to capture real time data. Potential risks and uncertainties are identified and ranked by adopting the analytical hierarchy process. The risk with the highest importance level is then included as an input parameter in formulating the warehouse operations workflow strategy using case-based reasoning. Through a pilot run in a Hong Kong-based machinery manufacturing company, it is found that the system helps to reduce both the planning lead time and the number of customer complaints regarding risk handling, and also allows monitoring of the warehouse performance