Our eyes are always in motion. Even during periods of relative fixation we produce so-called ‘fixational eye movements’, which include microsaccades, drift and tremor. Mental fatigue can modulate saccade dynamics, but its effects on microsaccades and drift are unknown. Here we asked human subjects to perform a prolonged and demanding visual search task (a simplified air traffic control task), with two difficulty levels, under both free-viewing and fixation conditions. Saccadic and microsaccadic velocity decreased with time-on-task whereas drift velocity increased, suggesting that ocular instability increases with mental fatigue. Task difficulty did not influence eye movements despite affecting reaction times, performance errors and subjective complexity ratings. We propose that variations in eye movement dynamics with time-on-task are consistent with the activation of the brain's sleep centers in correlation with mental fatigue. Covariation of saccadic and microsaccadic parameters moreover supports the hypothesis of a common generator for microsaccades and saccades. We conclude that changes in fixational and saccadic dynamics can indicate mental fatigue due to time-on-task, irrespective of task complexity. These findings suggest that fixational eye movement dynamics have the potential to signal the nervous system's activation state.