Frequency domain analyses in electromyographic (EMG) signals are frequently applied to assess muscle fatigue and similar variables. Moreover, Fourier-based approaches are typically used for investigating these procedures. Nonetheless, Fourier analysis assumes the signal as stationary which is unlikely during dynamic contractions. As an alternative method, wavelet-based treatments do not assume this pattern and may be considered as more appropriate for joint time-frequency domain analysis. Based on the previous statements, the purpose of the present study was to compare the application of Short-Time Fourier Transform (STFT) and Continuous Wavelet Transform (CWT) to assess muscle fatigue in dynamic exercise of a 1-km of cycling (time-trial condition). The results of this study indicated that CWT and STFT analyses have provided similar fatigue estimates (slope) (p > 0.05). However, CWT application represents lesser dispersion ( 0.05) according to different methods, it is important to note that these responses seem to show greater values for CWT compared to STFT for 2 superficial muscles. Thereby, we are capable of considering CWT as a reliable and useful method to take into consideration when non-stationary or oscillating exercise models are evaluated.