Recently, network security has become a major challenge in communication networks. Most wireless networks are exposed to some penetrative attacks such as signal interception, spoofing, and stray. Radio frequency (RF) fingerprinting is considered to be a promising solution for network security problems and has been applied with various improvements. In this paper, extensive data from Bluetooth (BT) devices are utilized in RF fingerprinting implementation. Hilbert-Huang transform (HHT) has been used, for the first time, for RF fingerprinting of Bluetooth (BT) device identification. In this way, time-frequency-energy distributions (TFED) are utilized. By means of the signals' energy envelopes, the transient signals are detected with some improvements. Thirteen features are extracted from the signals' transients along with their TFEDs. The extracted features are pre-processed to evaluate their usability. The implementation of three different classifiers to the extracted features is provided for the first time in this paper. A comparative analysis based on the receiver operating characteristics (ROC) curves, the associated areas under curves (AUC), and confusion matrix are obtained to visualize the performance of the applied classifiers. In doing this, different levels of signal to noise ratio (SNR) levels are used to evaluate the robustness of the extracted features and the classifier performances. The classification performance demonstrates the feasibility of the method. The results of this paper may help readers assess the usability of RF fingerprinting for BT signals at the physical layer security of wireless networks. INDEX TERMS Bluetooth, classification, Hilbert-Huang transform, network security, radio frequency fingerprinting, wireless networks.