Systems and methods for isolating a performance anomaly within one or more line replaceable units (LRUs) on a gas turbine engine by monitoring the start up transient are presented. The system comprises a set of sensors, an anomaly detector and a fault isolation reasoner. Each sensor of the set monitors at least one operating parameter of at least one engine component. The anomaly detector is configured to detect an anomaly in a component by comparing a particular value of an operating parameter to a base line value of that parameter. The specific cause of the startup anomaly is isolated utilizing a set of component reasoners that is based on the nature of the detected anomaly. The key events during the engine startup are identified by the combination of monitoring physically relevant phases of a startup and monitoring the engine control schedule. The values at these key events are used for comparing at the anomaly detector.