A method and apparatus for handling evolved universal terrestrial radio access network (E-UTRAN) radio access bearer (E-RAB) switch failure for dual connectivity in a wireless communication system is provided. A master evolved NodeB (MeNB) in dual connectivity receives an E-RAB modification confirm message including a list of E-RABs failed to be modified from a mobility management entity (MME). The MeNB may keep old general packet ratio service (GPRS) tunneling protocol (GTP) tunnels for the failed E-RABs, and trigger a secondary eNB (SeNB) release procedure or a SeNB modification procedure for releasing the failed E-RABs. Alternatively, the MeNB may trigger an E-RAB release procedure for releasing the failed E-RABs.