Provided is an electronic control unit (ECU) security function setting system including an ECU and a tester connected to the ECU through a communication network. The tester includes a security function requester configured to request a security function loader to the ECU when the ECU is in a security function setting mode; an user authenticator configured to receive a user authentication request from the ECU and perform an user authentication; and a firmware transmitter configured to transmit stored security function firmware to the ECU when the user authentication is passed, and the ECU activates an instruction present in the received security function firmware and perform a security function setting.