In some embodiments, a method of automatically setting a protocol is performed in a protocol automatic setting server communicating with a client in a Programmable Logic Controller (PLC) system. The method can include receiving a request frame from a client; analyzing a protocol of the request frame based on a protocol stack and determining a response frame corresponding to the request frame according to an analysis result; and transmitting the response frame to the client. The server can automatically analyze a request frame from the client based on the protocol stack, and thus conventional protocol presetting can be eliminated.