A method and system for encrypting data in a wireless communication system are provided. The system includes a first node for generating a first encryption key using a plurality of encryption key parameters when performing authentication with a second node, for changing a second parameter among the plurality of encryption key parameters to generate a second encryption key being identical to the first encryption key, if a first parameter among the plurality of encryption key parameters is changed during re-authentication between the first node and the second node, for generating the second encryption key using the changed first parameter and the changed second parameter, and for encrypting data to be transmitted to the second node using the second encryption key.