This invention relates to a user authenticating system and a method using aone-time fingerprint template. The system and the method according to the invention are improvements of the conventional user authentication based on the manner of comparing the fingerprint feature data only, for the purpose of preventing a false authentication by misusing fingerprint feature data, if exposed in the course of transfer thereof. In the system and the method according to the invention, fingerprint feature data of a user are combined with an OTT key transferred from a server. The combined result is encoded and transferred to an authenticating server. The authenticating server then confirms validity of the OTT key and authenticates the user based on the fingerprint. Thus, the present invention has an advantage of preventing a false authentication through hacking, etc., even if the OTT key is exposed to a network, because the OTT key is used only once for authentication.