An apparatus and method for controlling Tracking Area Update (TAU) in a wireless communication system are provided. A method for controlling TAU includes, in a case of receiving a request for TAU from a User Equipment (UE), determining a periodic TAU request count of the UE when a type of the TAU is periodic, deciding a TAU period of the UE based on the periodic TAU request count of the UE, and sending the UE a TAU response message including TAU period information of the UE.