Rotating machinery is fundamental in industry, gearboxes especially. However, failures may occur in their transmission components due to regular usage over long periods of time, even when operations are not intense. To avoid such failures, Structural Health Monitoring (SHM) techniques for damage prediction and in-advance detection can be applied. In this regard, correlations between measured signal variations and damage can be inspected using Artificial Intelligence (AI), which demands large numbers of data for training. Since obtaining signal samples of damaged components experimentally is currently unviable for complex systems due to destructive test costs, model-based numerical approaches are to be explored to solve this problem. To address this issue, this work applied an innovative hybrid Finite Element Method (FEM)–analytical approach, reducing computational effort and increasing performance with respect to traditional FEM. With this methodology, a system can be simulated with accuracy and without geometrical simplifications for healthy and damaged cases. Indeed, considering different positions and dimensions of damages (e.g., cracks) on the tooth roots of gears can offer new ways of damage investigation. As a reference to validate healthy systems and damage cases in terms of eigenfrequencies, a back-to-back test rig was used. Numerical simulations were performed for different cases, resulting in vibrational spectra for systems with no damage, with damage, and with damage of different intensities. The vibration spectra were used as data to train an Artificial Neural Network (ANN) to predict the machine state by Condition Monitoring (CM) and Fault Diagnosis (FD). For predicting the health and the intensity of damage to a system, classification and multi-class classification methods were implemented, respectively. Both sets of classification results presented good prediction agreement.