This study proposes supply chain business process analysis methods as well as a tool to evaluate the business process. With the progress in the sensor and actuator technologies, it becomes feasible to deal with information in the real space from the cyber space. The concept of this kind of environment is called Internet of Things (IoT). This study utilizes the EPC system, one of the networked RFID systems, an enabler of IoT and proposes a supply chain business process performance analysis and an anomaly analysis method. The study also proposes a tool to evaluate supply chain business process. It consists of agent simulator and real EPC system implementation and is able to realize supply chain business process flexibly. With this tool, the proposed methods are evaluated, and the effectiveness of them is confirmed.