Fatigue increases the risk of injury during sports training and rehabilitation. Early detection of fatigue during exercises would help adapt the training in order to prevent over-training and injury. This study lays the foundation for a data-driven model to automatically predict the onset of fatigue and quantify consequent fatigue changes using a force plate (FP) or inertial measurement units (IMUs). The force plate and body-worn IMUs were used to capture movements associated with exercises (squats, high knee jacks, and corkscrew toe-touch) to estimate participant-specific fatigue levels in a continuous fashion using random forest (RF) regression and convolutional neural network (CNN) based regression models. Analysis of unseen data showed high correlation (up to 89%, 93%, and 94% for the squat, jack, and corkscrew exercises, respectively) between the predicted fatigue levels and self-reported fatigue levels. Predictions using force plate data achieved similar performance as those with IMU data; the best results in both cases were achieved with a convolutional neural network. The displacement of the center of pressure (COP) was found to be correlated with fatigue compared to other commonly used features of the force plate. Bland–Altman analysis also confirmed that the predicted fatigue levels were close to the true values. These results contribute to the field of human motion recognition by proposing a deep neural network model that can detect fairly small changes of motion data in a continuous process and quantify the movement. Based on the successful findings with three different exercises, the general nature of the methodology is potentially applicable to a variety of other forms of exercises, thereby contributing to the future adaptation of exercise programs and prevention of over-training and injury as a result of excessive fatigue.