Mental fatigue (MF) is commonly observed following prolonged cognitive activity and can have major repercussions on the daily life of patients as well as healthy individuals. Despite its important impact, the cognitive processes involved in MF remain largely unknown. An influential hypothesis states that MF does not arise from a disruption of overused neural processes but, rather, is caused by a progressive decrease in motivation-related task engagement. Here, to test this hypothesis, we measured various neural, autonomic, psychometric and behavioral signatures of MF and motivation (EEG, ECG, pupil size, eye blinks, Skin conductance responses (SCRs), questionnaires and performance in a working memory (WM) task) in healthy volunteers, while MF was induced by Sudoku tasks performed for 120 min. Moreover extrinsic motivation was manipulated by using different levels of monetary reward. We found that, during the course of the experiment, the participants' subjective feeling of fatigue increased and their performance worsened while their blink rate and heart rate variability (HRV) increased. Conversely, reward-induced EEG, pupillometric and skin conductance signal changes, regarded as indicators of task engagement, remained constant during the experiment, and failed to correlate with the indices of MF. In addition, MF did not affect a simple reaction time task, despite the strong influence of extrinsic motivation on this task. Finally, alterations of the motivational state through monetary incentives failed to compensate the effects of MF. These findings indicate that MF in healthy subjects is not caused by an alteration of task engagement but is likely to be the consequence of a decrease in the efficiency, or availability, of cognitive resources.