Impairment of cognitive performance is often observed in time-on tasks. Theoretical considerations suggest that especially prefrontal cortex cognitive control functions is affected by time-on-task effects, but the role of effort/task engagement is not understood. We examine time-on-task effects in cognitive control on a neurophysiological level using a working-memory modulated response inhibition task and inter-relate prefrontal neuroanatomical region-specific theta-band activity with pupil diameter data using EEG-beamforming approaches. We show that task performance declines with time-on tasks, which was paralleled by a concomitant decreases of task-evoked superior frontal gyrus theta-band activity and a reduction in phasic pupil diameter modulations. A strong relation between cognitive control-related superior frontal theta-band activity and effort/task engagement indexed by phasic pupil diameter modulations was observed in the beginning of the experiment, especially for tasks requiring inhibitory controls and demanding high working memory. This strong relation vanished at the end of the experiment, suggesting a decoupling of cognitive control resources useable for a task and effort invested that characterizes time-on-task effects in prefrontal cortical structures.