A method of handling a radio link failure in a multiple-carrier system performed by a user equipment (UE) is provided. The method includes transmitting, to a base station (BS), a first message indicating a first radio link problem (RLP) in a first carrier when the first RLP is detected, transmitting, to the BS, a second message indicating a second RLP in a second carrier when the second RLP is detected, and transmitting, to the BS, a final message requesting a connection re-establishment with the BS. By using a plurality of different timers on CCs configured for one UE, the meaning of RLF in a multiple-carrier system for triggering radio connection re-establishment procedure is clarified and defined in detail.