A method is presented for controlling timers in a wireless communication system. When an idle mode signaling reduction (ISR) function of a user equipment (UE) is activated in the UE, a periodic tracking area update (P-TAU) timer and a periodic routing area update (P-RAU) timer are started. The P-TAU timer and the P-RAU timer run in the UE for updating a Mobility Management Entity (MME) and a Serving General packet radio service Support Node (SGSN) independently. The ISR function is activated when an update message activating the ISR function is received by the UE. When the P-TAU timer expires and the UE cannot initiate a tracking area update (TAU) procedure as a mobility management backoff (MM-BO) timer is running, a deactivate ISR timer corresponding to a first type network is started. The MM-BO timer is a timer configured to start when a MM-BO time value is received in the UE.