Demanding tasks like cognitive flexibility show time-related deterioration of performance (i.e. fatigability effects). Fatigability has been associated with structural and functional properties of the prefrontal cortex. However, the electrophysiological underpinnings of these processes are not well understood. We examined n = 34 healthy participants with a task switching paradigm in which switches were either signaled by cues or needed to be maintained by working memory processes. We analyzed event-related potentials (ERPs) and performed residue iteration decomposition (RIDE) to account for effects of fatigue on intra-individual variability of neurophysiological data. This was combined with source localization methods. We show that task switching is affected by time on task (TOT) effects mostly when working memory processes are needed. On a neurophysiological level, this effect could not be observed in standard ERPs, but only after accounting for intra-individual variability using RIDE. The RIDE data suggests that during task switching, fatigability specifically affects response recoding processes that are associated with functions of the middle frontal gyrus (MFG; BA10). The results underline propositions of the 'opportunity cost model', which states that fatigability effects of executive functions depend on the degree to which tasks engage similar prefrontal regions - in this case working memory and task switching mechanisms.