An apparatus and method for protecting radio frequency identification (RFID) data in a communication between a RFID tag and a RFID reader are provided. In the apparatus and method for protecting RFID data, message header information transmitted while communicating the RFID tag and the RFID reader is used to perform an encryption operation for important data, thereby protecting the important data included in the RFID tag. In the present invention, information of the RFID tag can be protected from an illegitimate eavesdropper and an ill-intentioned and unusual message can be detected, thereby ensuring the security of a RFID system.