Provided are an apparatus and method for managing security contents using a virtual folder. The apparatus for managing security contents includes a data control unit that receives an authority policy on contents from a security content server, and stores the received authority policy in a storage means, a security processing unit that encodes or decodes the contents based on the authority policy provided from the data control unit, and a security filesystem interface unit that creates a virtual folder based on position information of a folder to be virtualized and path information of the virtual folder by driving a virtual folder creation module that is operated in a kernel mode and registers the created virtual folder in a filesystem, and provides, to the security processing unit, contents corresponding to an input and output event for contents which have been recorded or are to be recorded in the virtual folder hooked from the kernel mode and instructs the security processing unit to encode or decode the provided contents. According to the present invention, it is possible to provide contents created in different environments to a user based on authority information without any separate content conversion operation.