Uncertainty analysis of an Artificial Neural Network (ANN) based method for spectral analysis of asynchronously sampled signals is performed. Main uncer-tainty components contributions, jitter and quantization noise, are considered in order to obtain the signal amplitude and phase uncertainties using Monte Carlo method. The analysis performed identifies also uncertainties main contributions depending on parameters configurations. The analysis is performed simultane-ously with the proposed method and two others: Discrete Fourier Transform (DFT) and Multiharmonic Sine Fitting Method (MSFM), in order to compare them in terms of uncertainty. Results show the proposed method has the same uncertainty as DFT for amplitude values and around double uncertainty in phase values.