A method and apparatus for performing a partial handover procedure in a wireless communication system is provided. An eNodeB (eNB) of a 3rd generation partnership project (3GPP) long term evolution (LTE) system determines E-UTRAN radio access bearers (E-RABs) to be offloaded to an access point (AP) of a wireless local area network (WLAN) system, and transmits an E-RAB release indication message, which includes a list of the E-RABs to be offloaded to the AP and a corresponding cause which is set to “Offload to WLAN”, to a mobility management entity (MME) of the 3GPP LTE system.