Physical fatigue accounts for many injuries in the workplace, sports arena, or battlefield. The traditional approaches to monitor fatigue rely on detecting and measuring shifts in the person’s muscular surface electromyography (sEMG) signals. However, assessing neuromuscular fatigue based purely on sEMG signals fails to account for the changing muscle dynamics during long dynamic physical tasks. To combat this dilemma, a system-based methodology has been recently developed and applied to several upper-extremity tasks. In this paper, we validate the efficacy of this novel methodology on the lower extremities during a dynamic activity. Specifically, the system-based monitoring methodology was applied to a cycling endurance task. It was statistically demonstrated that the system-based methodology resulted in a more-sensitive and less noisy metric, in comparison with an EMG-based methodology. The efficacy of the methodology was further illustrated by analyzing the inter-segmental recovering and fatiguing trends, which aligned with each muscle’s expected inter-muscle synergistic relationship.