Fault detection and isolation in unmanned aerial vehicle (UAV) propellers are critical for operational safety and efficiency. Most existing fault diagnosis techniques rely basically on traditional statistical-based methods that necessitate better approaches. This study explores the application of untraditional feature extraction methodologies, namely Permutation Entropy (PE), Lempel–Ziv Complexity (LZC), and Teager–Kaiser Energy Operator (TKEO), on the PADRE dataset, which encapsulates various rotor fault configurations. The extracted features were subjected to a Chi-Square (χ2) feature selection process to identify the most significant features for input into a Deep Neural Network. The Taguchi method was utilized to test the performance of the recorded features, correspondingly. Performance metrics, including Accuracy, F1-Score, Precision, and Recall, were employed to evaluate the model’s effectiveness before and after the feature selection. The achieved accuracy has increased by 0.9% when compared with results utilizing traditional statistical methods. Comparative analysis with prior research reveals that the proposed untraditional features surpass traditional methods in diagnosing UAV propeller faults. It resulted in improved performance metrics with Accuracy, F1-Score, Precision, and Recall reaching 99.6%, 99.5%, 99.5%, and 99.5%, respectively. The results suggest promising directions for future research in UAV maintenance and safety protocols.