There has been a substantial increase in scientific investigations into the neural underpinnings of acute mental fatigue (AMF). These functional magnetic resonance imaging (fMRI) studies found that altered activation in the insula, dorsolateral prefrontal cortex, and anterior cingulate cortex is associated with the decline in behavioural performance caused by AMF. Performance changes induced by AMF are often characterized by fluctuations, the functional basis of which remains insufficiently understood. Our study aimed to investigate the neural alterations that might be responsible for these performance fluctuations. We used the 15-minute long Psychomotor Vigilance Task (PVT) to induce AMF through the time-on-task effect, and fMRI to detect the fluctuations in task performance in healthy young people. To capture individual differences in performance stability, the standard deviation of reaction speed (SD Speed) per minute was used for each participant to model performance fluctuations in subject-level fMRI analyses. The 15-minute SD Speed was used as dependent variable in post hoc brain-behaviour regression analyses. Our findings revealed that the task performance fluctuations during the PVT were related to deactivation of three clusters of regions: the right middle and inferior frontal gyri (Cluster 1), the left superior, middle and medial frontal gyri (Cluster 2), and the right precuneus and posterior cingulate gyrus (Cluster 3). Additionally, post hoc regression analysis revealed that increased deactivation in Clusters 1 and 2 predicted higher perfromance fluctuations during the PVT. Our findings supplement previous ones on AMF as frontal regions are involved in the „cost-benefit” assessment of tasks related to mental fatigue.