Mental fatigue has traditionally been defined as a condition of reduced cognitive efficiency and performance, accompanied by a subjective feeling of fatigue. Even though we could expect to find associations between the three defining characteristic of mental fatigue (performance impairment, physiological deactivation and subjective fatigue), research has shown that the emergence of inconsistencies between measures is more frequent than one might expect: people proved capable of maintaining adequate performance levels even after having declared themselves fatigued. This could be explained under the compensatory control mechanism models, which state that humans are able to provide additional resources under demanding conditions, but only at the expense of psychophysiological cost and subjective fatigue. We tested this explanation by manipulating task complexity and time performing a simulated air-traffic control task. We collected psychophysiological, performance and subjective data. A decrease in pupil size was seen in the low-aircraft-density condition, while pupil size remained constant in the high-aircraft-density condition. Participants’ task performance was optimal in both conditions, though they showed an increase in subjective feelings of fatigue, especially in the high-complexity task condition. Thus, complexity seemed to trigger compensatory mechanisms, which reallocated extra resources that physiologically activated participants in order to deal with a higher complexity task, whereas subjective fatigue could be acting as a signal to the organism of impending resource depletion. Our findings support compensatory control theories and offer an explanation of inconsistencies between fatigue measures. Further research on compensatory mechanisms is needed to enable better management of fatigue effects to prevent work-related accidents.