In an era of tremendous development in information technology and the Internet of Things (IoT), security plays a key role in safety devices connected with the Internet. Authentication is vital in the security field, and to achieve a strong authentication scheme, there are several systems using a Multi-Factor Authentication (MFA) scheme based on a smart card, token, and biometric. However, these schemes have suffered from the extra cost; lost, stolen or broken factor, and malicious attacks. In this paper, we design an MFA protocol to be the authenticated administrator of IoT’s devices. The main components of our protocol are a smart mobile device and the fuzzy extractor of the administrator’s fingerprint. The information of the authenticated user is stored in an anomalous manner in mobile devices and servers to resist well-known attacks, and, as a result, the attacker fails to authenticate the system when they obtain a mobile device or password. Our work overcomes the above-mentioned issues and does not require extra cost for a fingerprint device. By using the AVISPA tool to analysis protocol security, the results are good and safe against known attacks.