A method for controlling a transparent tunnel mode operation in a Wireless Dockee (WD) in a communication system supporting a wireless docking protocol is provided. The method includes performing a group join process and a provisioning process for security keys with a Wireless Docking Center (WDC); accessing services of a Wireless Docking Environment (WDN); selecting an operating mode between the WD and the WDC as a transparent tunnel mode; performing a process of getting information related to a peripheral with the WDC; requesting the WDC to enable a monitor mode and a promiscuous mode; and transmitting/receiving a data packet using the information related to the peripheral with the peripheral if a Miracast connection and a docking session are established between the WD and the peripheral.