An apparatus and method for selecting a Secure Element (SE) in a Near Field Communication (NFC) device are provided. Identifiers (IDs) are displayed to indicate which application programs correspond to a plurality of SEs. Upon selection of one of the IDs, an SE corresponding to the selected application-program ID from among the plurality of SEs is activated. An NFC controller is configured to select an SE from one of at least three schemes including a User Selection Scheme, Automatic Selection Scheme, and a Hybrid Scheme.