A transient fault detection system and method is provided that facilitates improved fault detection performance in transient conditions. The transient fault detection system provides the ability to detect symptoms of fault in engine that occur in transient conditions. The transient fault detection system includes a feature extractor that measures sensor data during transient conditions and extracts salient features from the measured sensor data. The extracted salient features are passed to a classifier that analyzes the extracted salient features to determine if a fault has occurred during the transient conditions. Detected faults can then be passed to a diagnostic system where they can be passed as appropriate to maintenance personnel.