Frequency domain analyses of changes in electromyographic (EMG) signals over time are frequently used to assess muscle fatigue. Fourier based approaches are typically used in these analyses, yet Fourier analysis assumes signal stationarity, which is unlikely during dynamic contractions. Wavelet based methods of signal analysis do not assume stationarity and may be more appropriate for joint time-frequency domain analysis. The purpose of this study was to compare Short-Time Fourier Transform (STFT) and Continuous Wavelet Transform (CWT) in assessing muscle fatigue in supramaximal constant load dynamic exercise (110% VO(2peak)). The results of this study indicate that CWT and STFT analyses give similar fatigue estimates (slope of median frequency) in supramaximal constant load dynamic exercise (P>0.05). However, the results of the variance was significantly lower for at least one of the muscles studied in CWT compared to STFT (P < 0.05) indicating more variability in the EMG signal analysis using STFT. Thus, the stationarity assumption may not be the sole factor responsible for affecting the Fourier based estimates.