Reduced maximal force capability of skeletal muscle, as a consequence of exercise, can be due to peripheral or central fatigue mechanisms. In upper-limb muscles, neuromuscular fatigue is concurrent with reduced corticospinal excitability and increased inhibition (lengthened corticospinal silent period [CSP]; reduced short-interval intracortical inhibition [SICI] ratio). However, it is unclear whether these adjustments occur in response to fatiguing exercise of locomotor muscles. This study examined the effect of fatiguing, maximal, knee-extensor exercise on motor cortical excitability and inhibition. Thirteen males performed three 30-s maximal, isometric contractions with the dominant knee-extensors (MVC1, MVC2 and MVC3), separated by 60 s. At the end of, and between each MVC, neuromuscular fatigue, corticospinal excitability, CSP and SICI were assessed with supramaximal stimulation of the femoral nerve, and motor cortical stimulation, respectively. Repeated MVCs caused progressive reductions in MVC (− 10, − 24 and − 29%, respectively, P ≤ 0.01), along with significant peripheral (reductions in potentiated twitch of − 23, −53 and − 60%, respectively, P < 0.001) and central (reductions in VA of − 10% and − 13% post-MVC2 and 3, respectively, P ≤ 0.01) fatigue. Following MVC1 corticospinal excitability was reduced, and remained depressed thereafter. CSP increased in duration and remained longer throughout the protocol; whereas, no change in SICI was observed. Repeated, sustained, maximal contractions of the knee-extensors elicited substantial peripheral and central fatigue that was accompanied by a concomitant reduction in corticospinal excitability. However, divergent responses exist between inhibitory networks within the motor cortex, the activity of inhibitory networks mediated by GABAB are increased, whereas those mediated by GABAA are not.