Despite the growing use of independent component analysis (ICA) algorithms for isolating and removing eyeblink‐related activity from EEG data, we have limited understanding of how variability associated with ICA uncertainty may be influencing the reconstructed EEG signal after removing the eyeblink artifact components. To characterize the magnitude of this ICA uncertainty and to understand the extent to which it may influence findings within ERP and EEG investigations, ICA decompositions of EEG data from 32 college‐aged young adults were repeated 30 times for three popular ICA algorithms. Following each decomposition, eyeblink components were identified and removed. The remaining components were back‐projected, and the resulting clean EEG data were further used to analyze ERPs. Findings revealed that ICA uncertainty results in variation in P3 amplitude as well as variation across all EEG sampling points, but differs across ICA algorithms as a function of the spatial location of the EEG channel. This investigation highlights the potential of ICA uncertainty to introduce additional sources of variance when the data are back‐projected without artifact components. Careful selection of ICA algorithms and parameters can reduce the extent to which ICA uncertainty may introduce an additional source of variance within ERP/EEG studies.