Cognitive fatigue (CF) is a critical factor affecting performance and well-being. It can be altered in suboptimal sleep quality conditions, e.g., in patients suffering from obstructive sleep apnea who experience both intermittent hypoxia and sleep fragmentation (SF). Understanding the neurophysiological basis of SF in healthy individuals can provide insights to improve cognitive functioning in disrupted sleep conditions. In this electroencephalographical (EEG) study, we investigated in 16 healthy young participants the impact of experimentally induced SF on the neurophysiological correlates of CF measured before, during, and after practice on the TloadDback, a working memory task tailored to each individual's maximal cognitive resources. The participants spent three consecutive nights in the laboratory two times, once in an undisrupted sleep (UdS) condition and once in an SF condition induced by non-awakening auditory stimulations, counterbalanced and performed the TloadDback task both in a high (HCL) and a low (LCL) cognitive load condition. EEG activity was recorded during wakefulness in the 5 min resting state immediately before and after, as well as during the 16 min of the TloadDback task practice. In the high cognitive load under a sleep-fragmentation (HCL/SF) condition, high beta power increased during the TloadDback, indicating heightened cognitive effort, and the beta and alpha power increased in the post- vs. pre-task resting state, suggesting a relaxation rebound. In the low cognitive load/undisturbed sleep (LCL/UdS) condition, low beta activity increased, suggesting a relaxed focus, as well as mid beta activity associated with active thinking. These findings highlight the dynamic impact of SF on the neurophysiological correlates of CF and underscore the importance of sleep quality and continuity to maintain optimal cognitive functioning.