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This paper investigates a torque estimation method for muscle fatigue tracking, using stimulus evoked electromyography (eEMG) in the context of a functional electrical stimulation (FES) rehabilitation system. Although FES is able to effectively restore motor function in spinal cord injured (SCI) individuals, its application is inevitably restricted by muscle fatigue. In addition, the sensory feedback indicating fatigue is missing in such patients. Therefore, torque estimation is essential to provide feedback or feedforward signal for adaptive FES control. In this paper, a fatigue-inducing protocol is conducted on five SCI subjects via transcutaneous electrodes under isometric condition, and eEMG signals are collected by surface electrodes. A myoelectrical mechanical muscle model based on the Hammerstein structure with eEMG as model input is employed to capture muscle contraction dynamics. It is demonstrated that the correlation between eEMG and torque is time varying during muscle fatigue. Compared to conventional fixed-parameter models, the adapted-parameter model shows better torque prediction performance in fatiguing muscles. It motivates us to use a Kalman filter with forgetting factor for estimating the time-varying parameters and for tracking muscle fatigue. The assessment with experimental data reveals that the identified eEMG-to-torque model properly predicts fatiguing muscle behavior. Furthermore, the performance of the time-varying parameter estimation is efficient, suggesting that real-time tracking is feasible with a Kalman filter and driven by eEMG sensing in the application of FES.