A method and apparatus for configuring radio resources for a device-to-device (D2D) operation in a wireless communication system is provided. A user equipment (UE) configures two types of radio resources which include a first type of radio resources and a second type of radio resources. The first type of radio resources is used for the D2D communication, and the second type of radio resources is used for communication between the UE and a network. Then, the UE performs the D2D communication by using the first type of radio resources upon receiving a D2D radio network temporary identifier (D-RNTI) for the D2D communication.