An embodiment discloses an electronic device capable of performing an upgrade to an Operating System (OS) having enhanced security without deleting any user data in an electronic device having an OS and a method of operating the same. An embodiment discloses a method of upgrading an OS of an electronic device. The method includes detecting operating system upgrade initiation. The method also includes generating labeling information on each piece of user data; and relabeling the user data based on the labeling information.