A method and system for updating or upgrading firmware of a RFID reader installed in an access control system are provided. The reader includes a microcontroller unit that performs method steps automatically, including checking periodically whether an update file is stored in a designated storage location. If the update file is found, the microcontroller unit reads the update file and then performs an update or upgrade process of its firmware based on the update file. The method of this invention improves use of remaining storage capacity in the RFID reader or associated devices.