A method and apparatus is capable of encrypting short data in a wireless communication system When a terminal generates a short data burst in idle mode, the apparatus generates a Traffic Encryption Key (TEK) using a Cipher-based Message Authentication Code (CMAC)-TEK prekey derived from an Authorization Key (AK) related to Security Association (SA) between the terminal and a Base Station (BS). A nonce is constructed with a Packet Number (PN) identical to an uplink CMAC PN (CMAC-PN_U) transmitted together with a Ranging Request (RNG-REQ) message carrying the short data burst The short data burst is encrypted using the TEK and the nonce. A Medium Access Control (MAC) Protocol Data Unit (PDU) is generated by attaching a MAC header and a CMAC digest for integrity protection to the RNG-REQ message carrying the encrypted short data burst. The MAC PDU is transmitted to the BS.