Background: Motor fatigue is common in multiple sclerosis (MS), but its pathophysiology is still poorly understood. Here we used functional magnetic resonance imaging (fMRI) to delineate how the acute induction of motor fatigue alters functional activity of the motor system and how these activity changes are related to motor fatigue. Method: Forty-four right-handed mildly disabled patients with relapsing-remitting MS and 25 healthy controls performed a maximal tonic precision grip with their right hand until they developed motor fatigue. Before and after the fatiguing task, participants performed a non-fatiguing tonic grip force task, producing 15–20% of their maximum grip force based on visual feedback. Task related brain activity was mapped with blood-oxygen level dependent fMRI at 3 T. Statistical parametric mapping was used to identify relative changes in task-related activation from the pre-fatigue to the recovery MRI session. Results: Following fatigue induction, task performance was perturbed in both groups, and task-related activation increased in the right (ipsilateral) primary motor hand area. In patients with MS, task-related activity increased bilaterally during the recovery phase in the ventrolateral portion of the middle putamen and lateral prefrontal cortex relative to controls. The more patients increased task-related activity in left dorsal premotor cortex after the fatiguing task, the less they experienced motor fatigue during daily life. Conclusion: Patients with MS show enhanced functional engagement of the associative cortico-basal ganglia loop following acute induction of motor fatigue in the contralateral hand. This may reflect increased mental effort to generate movements in the recovery phase after fatigue induction. The ability to recruit the contralateral dorsal premotor cortex after fatigue induction may constitute a protective mechanism against experiencing motor fatigue in everyday life.