Provided are a method and an apparatus for rebooting a computer system taking both security and user convenience into account. The computer system includes an authentication mode information storage unit storing authentication mode information related to an authentication mode when booting the computer system, a first driver sensing rebooting of the computer system and setting an authentication mode of the authentication mode information, and a second driver, which reads the authentication mode information and if the authentication mode is a first mode, performs rebooting without user authentication and if the authentication mode is a second mode, performs rebooting after user authentication.