A system and method for configuring a device using a remote controller are provided. The system includes at least one device which transmits and receives data using a wireless communication connection and performs a preset operation according to a received control signal; a server which communicates data with the at least one device over a radio channel and controls functions of the at least one device; and a short distance wireless communication device that authenticates the at least one device by receiving a device address list through radio communications with the server and assigning a device address selected from the received address list to the at least one device. Thus, inputting password information of the device directly to the server is not required when a new device is configured.