Understanding the effects of fatigue is a central issue in the context of endurance sports. Given the popularity of running, there are numerous novices among runners. Therefore, understanding the effects of fatigue in novice runners is an important issue. Various studies have drawn conclusions about the control of certain variables by analyzing motor variability. One variable that plays a crucial role during running is the center of mass (CoM), as it reflects the movement of the whole body in a simplified way. Therefore, the aim of this study was to analyze the effects of fatigue on the motor variability structure that stabilizes the CoM trajectory in novice runners. To do so, the uncontrolled manifold approach was applied to a 3D whole-body model using the CoM as the result variable. It was found that motor variability increased with fatigue (UCMꓕ). However, the UCMRatio did not change. This indicates that the control of the CoM decreased, whereas the stability was not affected. The decreases in control were correlated with the degree of exhaustion, as indicated by the Borg scale (during breaking and flight phase). It can be summarized that running-induced fatigue increases the step-to-step variability in novice runners and affects the control of their CoM.