The present invention provides a method for handling a handover procedure for a Radio Resource Control (RRC) layer in a user equipment (UE) of a wireless communication system. The method includes steps of indicating occurrence of a handover procedure to a Packet Data Convergence Protocol (PDCP) layer of the UE when receiving an RRC Connection Reconfiguration message for triggering the handover procedure, applying a new security configuration to the PDCP layer if the RRC Connection Reconfiguration message includes an information element (IE) for providing the security configuration, and requesting a Medium Access Control (MAC) layer of the UE to initiate a random access procedure for the handover procedure.