An authentication system with an automatic authentication mechanism and an automatic authentication method are provided. The authentication system includes a server device and a gateway device. The gateway device is coupled to the server device. The gateway device is configured to act as a fast identity online (FIDO) client to send a gateway device registration data to register the gateway device in the server device acting as a FIDO server, and then the gateway device defines itself as initialized and connected. The gateway device periodically sends data to server device for authentication to maintain a trusted connection between the server device and the gateway device.