This article proposes a novel and effective solution for estimating fatigue life of General Aviation (GA) airframes using flight data produced by digital avionics systems, which are being installed or retrofitted into a growing number of GA aircraft. In the proposed implementation, a flight dynamics model is adopted to process the recorded flight data and to determine the dynamic loadings experienced by the aircraft. The equivalent loading cycles at fatigue-critical points of the primary structure are counted by means of statistical methods. For validation purposes, the developed approach is applied to flight data recorded by a fleet of Cessna 172S aircraft fitted with a Garmin G1000 integrated navigation and guidance system. Based on the initial experimental results and the developed uncertainty analysis, the proposed approach provides acceptable estimates of the residual fatigue life of the aircraft, thereby allowing a cost-effective and streamlined structural integrity monitoring solution. Future developments will address the possible adoption of the proposed method for unmanned aircraft structural health monitoring, also considering the accuracy enhancements achievable with advanced navigation and guidance architectures based on Global Navigation Satellite Systems (GNSS), Vision-Based Navigation (VBN) Sensors, Inertial Measurement Units (IMU) and Aircraft Dynamics Model (ADM) augmentation.