This pilot study aimed to explore a method for characterization of the electromyogram frequency spectrum during a sustained exertion task, performed by the upper limb. Methods: Nine participants underwent an isometric localized muscle fatigue protocol on an isokinetic dynamometer until exhaustion, while monitored with surface electromyography (sEMG) of the shoulder’s external rotators. Firstly, three methods of signal energy analysis based on primer frequency contributors were compared to the energy of the entire spectrum. Secondly, the chosen method of analysis was used to characterize the signal energy at beginning (T1), in the middle (T2) and at the end (T3) of the fatigue protocol and compared to the torque output and the shift in the median frequencies during the trial. Results: There were statistically significant differences between T1 and T3 for signal energy (p < 0.007) and for central frequency of the interval (p = 0.003). Moreover, the isometric peak torque was also different between T1 and T3 (p < 0.001). Overall, there were no differences between the signal energy enclosed in the 40 primer frequency contributors and the analysis of the full spectrum energy; consequently, it was the method of choice. The reported fatigue and the decrease in the produced muscle torque was consistent with fatigue-induced alterations in the electromyogram frequency spectrum. In conclusion, the developed protocol has potential to be considered as an easy-to-use method for EMG-based analysis of isometric muscle exertion until fatigue. Thus, the novelty of the proposed method is to explore, in muscle fatigue, the use of only the main contributors in the frequency domain of the EMG spectrum, avoiding surplus information, that may not represent muscle functioning. However, further studies are needed to investigate the stability of the present findings in a more comprehensive sample.