A clipboard protection system for protecting data stored in a clipboard in conjunction with a clipboard management system for storing, extracting and transferring data independently from an application as a basic function of an operating system, the clipboard protection system comprising: an identification information management unit for, when an object desiring to store data in the clipboard is a reliable object, changing first identification information assigned to data to be stored in the clipboard into preset second identification information, managing the second identification information, and outputting second identification information corresponding to identification information of read target data requested to be extracted when the reliable object requests extraction of data stored in the clipboard; a data protection unit for encrypting and outputting data to be stored in the clipboard, and decrypting and outputting encrypted data read from the clipboard; a control unit for requesting the clipboard management system to record encrypted security data in the clipboard in conjunction with the second identification information, characterised in that: the control unit requests to determine whether the identification information of the read target data is present if a request to extract data stored in the clipboard is received from the reliable object, wherein the control unit transfers second identification information corresponding to the identification information of the read target data to the clipboard management system, and requesting the clipboard management system to read encrypted security data from the clipboard using the second identification information and provide the encrypted security data if a response indicating that the identification information of the read target data is not present is received in response to the request, and wherein the control unit requests the clipboard management system to read the read target data from the clipboard without using the second identification information and provide the read target data if a response indicating that the identification information of the read target data is present is received in response to the request. an identification information management unit for, when an object desiring to store data in the clipboard is a reliable object, changing first identification information assigned to data to be stored in the clipboard into preset second identification information, managing the second identification information, and outputting second identification information corresponding to identification information of read target data requested to be extracted when the reliable object requests extraction of data stored in the clipboard; a data protection unit for encrypting and outputting data to be stored in the clipboard, and decrypting and outputting encrypted data read from the clipboard; a control unit for requesting the clipboard management system to record encrypted security data in the clipboard in conjunction with the second identification information, characterised in that: the control unit requests to determine whether the identification information of the read target data is present if a request to extract data stored in the clipboard is received from the reliable object, wherein the control unit transfers second identification information corresponding to the identification information of the read target data to the clipboard management system, and requesting the clipboard management system to read encrypted security data from the clipboard using the second identification information and provide the encrypted security data if a response indicating that the identification information of the read target data is not present is received in response to the request, and wherein the control unit requests the clipboard management system to read the read target data from the clipboard without using the second identification information and provide the read target data if a response indicating that the identification information of the read target data is present is received in response to the request. the control unit requests to determine whether the identification information of the read target data is present if a request to extract data stored in the clipboard is received from the reliable object, wherein the control unit transfers second identification information corresponding to the identification information of the read target data to the clipboard management system, and requesting the clipboard management system to read encrypted security data from the clipboard using the second identification information and provide the encrypted security data if a response indicating that the identification information of the read target data is not present is received in response to the request, and wherein the control unit requests the clipboard management system to read the read target data from the clipboard without using the second identification information and provide the read target data if a response indicating that the identification information of the read target data is present is received in response to the request.