A system for operating a workflow and a method applied to the system are proposed, so as to conduct an electronic workflow for an enterprise based on a server/client architecture in a intranet or internet environment. A terminal device of the system allows a user at the terminal device to submit a request for inquiring, browsing, issuing or reading a document, which is transmitted a network server for initiating a service server, so as to process the request and transmit the processed result through the network server to the user. The foregoing system and method can substitute for a conventional system in manual processing and is a powerful tool to fulfill the objectives for an enterprise in promoting the working efficiency and reducing the management cost.