This paper presents research that investigated the effects of mental fatigue on brain activity using electroencephalogram (EEG) signals. Since EEG signals are considered to be non-stationary, time-frequency analysis has frequently been used for analysis. The S-transform is a time-frequency analysis method and is used in this paper to analyze EEG signals during alert and fatigue states during a driving simulator task. Repeated-measure MANOVA results show significant differences between alert and fatigue states within the alpha (8-13Hz) frequency band. The two sites demonstrating the greatest increases in alpha activity during fatigue were the Cz and P4 sites. The results show that S-transform analysis can be used to distinguish between alert and fatigue states in the EEG and also supports the use of the S-transform for EEG analysis.