Abstract <p>The uniqueness of the electroencephalogram (EEG), a distinct biometric marker inherent to each individual, yields significant advantages for user authentication and identification in brain-computer interface (BCI) systems. However, EEG features can easily change according to the user’s state, which may affect the performance of biometric recognition systems based on EEG. Notably, in EEG data collection for such systems, fatigue levels can fluctuate over time—a factor that has yet to be thoroughly investigated concerning its impact on individual recognition performance. This study explores the implications of fatigue on EEG-based personal recognition systems. We derived six sub-datasets from two simulated driving datasets, each labeled with varying levels of fatigue. From each sub-dataset, we extracted six features for identity recognition within and across different fatigue levels. Single-session and cross-session studies revealed that the disparity of EEG fatigue levels between the training and testing sets increased, and system recognition accuracy experienced a decline. Specifically, recognition accuracy typically fell by over 30<InlineEquation ID="IEq1"> <EquationSource Format="TEX">\(\%\)</EquationSource> <EquationSource Format="MATHML"><math> <mo>%</mo> </math></EquationSource> </InlineEquation> after 90&#xa0;min of simulated driving. Furthermore, identity recognition results are better when the training set includes EEG in more fatigued states compared to the test set, rather than the other way around. Crucially, the method based on functional connectivity features shows the best recognition accuracy under different fatigue levels. This research emphasizes the potential benefits of considering fatigue variations in EEG-based personal recognition systems.</p> Graphical abstract <p></p>