In IoT networks, authentication of nodes is primordial and RF fingerprinting is one of the candidates as a non-cryptographic method. RF fingerprinting is a physical-layer security method consisting of authenticated wireless devices using their components’ impairments. In this paper, we propose the RF eigenfingerprints method, inspired by face recognition works called eigenfaces. Our method automatically learns important features using singular value decomposition (SVD), selects important ones using Ljung–Box test, and performs authentication based on a statistical model. We also propose simulation, real-world experiment, and FPGA implementation to highlight the performance of the method. Particularly, we propose a novel RF fingerprinting impairments model for simulation. The end of the paper is dedicated to a discussion about good properties of RF fingerprinting in IoT context, giving our method as an example. Indeed, RF eigenfingerprint has interesting properties such as good scalability, low complexity, and high explainability, making it a good candidate for implementation in IoT context.