Provided is a method of hiding a specified directory with no effect on compatibility with an existing file system. According to an aspect of the invention, an apparatus for managing a hidden area includes a hidden area generation unit which sets a portion of the data area as a hidden area and records meta data for the set hidden area, a hidden area release unit which moves a directory entry of a root directory of the hidden area into the directory entry area and returns a cluster recorded with the meta data to release the set hidden area, and an access control unit which controls an access to the hidden area when the hidden area is set.