The aim of this study was to examine the central neurophysiological mechanisms during fatigue induced by submaximal isometric contractions. A total of 23 individuals participated in the study and were assigned to fatigue and nonfatigue groups. Handgrip force, root mean square (RMS) of surface electromyography (sEMG) signal and movement-related cortical potentials during self-paced submaximal handgrip isometric contractions were assessed for each participant. The experimental data showed significant decreases in both maximal voluntary contraction [-24.3%; F(3, 42)=19.62, P<0.001, ηp=0.48] and RMS [-30.1%; F(3, 42)=19.01, P<0.001, ηp=0.57] during maximal voluntary contractions and a significant increase [F(3, 42)=14.27, P<0.001, ηp=0.50] in the average RMS of sEMG over four blocks in the fatigue group. There was no significant difference in the readiness potential between the fatigue and the nonfatigue groups at early stages, and at late stages, significant differences were observed only at the Fp1 and FC1 sites. Motor potential amplitudes were significantly higher in the fatigue group than in the nonfatigue group irrespective of block or electrode positions. Positive waveforms were observed in the prefrontal cortex in states without muscle fatigue, whereas a negative waveform pattern was observed with muscle fatigue. Significant within-subject correlations were observed between motor potential at the C1 site and RMS of sEMG (r=-0.439, P=0.02, ηp=0.11). Neurophysiological evidence indicates that cortical activity increases in the prefrontal cortex, primary motor cortex and supplementary motor cortex with muscle fatigue. Muscle fatigue appears to have considerable effects on the components of movement-related cortical potentials during movement execution, whereas the readiness potential before movement is sensitive to cognitive demands during prolonged exercise. Our results provide additional evidence for a link between central motor command during movement execution and motor unit recruitment.