Advanced engine health monitoring and diagnostic systems greatly benefit users helping them avoid potentially expensive and time-consuming repairs by proactively identifying shifts in engine performance trends and proposing optimal maintenance decisions. Engine health deterioration can manifest itself in terms of rapid and gradual performance deviations. The former is due to a fault event that results in a short-term performance shift and is usually concentrated in a single component. Whereas the latter implies a gradual performance loss that develops slowly and simultaneously in all engine components over their lifetime due to wear and tear. An effective engine lifecycle monitoring and diagnostic system is therefore required to be capable of discriminating these two deterioration mechanisms followed by isolating and identifying the rapid fault accurately. In the proposed solution, this diagnostic problem is addressed through a combination of adaptive gas path analysis and artificial neural networks. The gas path analysis is applied to predict performance trends in the form of isentropic efficiency and flow capacity residuals that provide preliminary information about the deterioration type. Sets of neural network modules are trained to filter out noise in the measurements, discriminate rapid and gradual faults, and identify the nature of the root cause, in an integrated manner with the gas path analysis. The performance of the proposed integrated method has been demonstrated and validated based on performance data obtained from a three-shaft turbofan engine. The improvement achieved by the combined approach over the gas path analysis technique alone would strengthen the relevance and long-term impact of our proposed method in the gas turbine industry. © 2021, Prognostics and Health Management Society. All rights reserved.