A method and system for user authentication by using an authentication virtual code are provided. A user authentication method using an authentication virtual code includes receiving, by a server, the authentication virtual code, searching, by the server, for an authentication card storage location, at which the authentication card is registered, in a storage location search algorithm based on the authentication virtual code, identifying, by the server, a user by extracting user information stored after being matched with the found authentication card storage location, verifying, by the server, an authentication virtual code based on a time point at which the authentication virtual code is received, and approving, by the server, user authentication.