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This article investigates the neutral voltage difference signal, VNO signal, for fault diagnosis. The aforementioned signal is the signal of the voltage between the common star point of the stator and the common star point of the load. The under-study faults are demagnetization and static eccentricity faults, while the machine in which the faults are investigated is an axial flux permanent magnet (AFPM) synchronous generator, suitable for wind power applications. This study was conducted using a 3D finite element method (3D-FEM), and the machine’s FEM model was validated through experiments. This method is one of the most accurate methods for electrical machine computation, allowing for a detailed study of electromagnetic behavior. The components that constitute the VNO signal were determined using a 3D-FEM software program (Opera 18R2). Subsequently, further analysis was performed using MATLAB R2022b software, and a fast Fourier transform (FFT) was applied to this signal. In all the investigated faulty cases, new harmonics appeared, and the healthy amplitudes of most of the already existing harmonics increased. These findings can be used for fault identification. The analysis revealed that the harmonic frequency of 1.5fs was the most dominant in the case of demagnetization, while in the case of static eccentricity, the most dominant harmonic was a frequency equal to the machine’s operating frequency, fs. The novelty of this study is that this signal has not previously been used for fault identification, especially in AFPM synchronous machines. This signal depends on EMF voltage and stator phase currents but is less sinusoidal. Consequently, it can detect faults in cases where the aforementioned signals cannot be used for detection.