Sleep deprivation leads to impairments in cognitive function. Here, we tested the hypothesis that cognitive changes in the sleep-deprived brain may be explained by information processing within and between large scale cortical networks. We acquired functional magnetic resonance imaging (fMRI) scans of 20 healthy volunteers during attention and executive tasks following a regular night of sleep, a night of sleep deprivation, and a recovery nap. Overall, sleep deprivation is associated with increased cortex-wide integration, driven by greater within network integration. The relative ration of within-between network integration in the sleep deprived state was tightly associated with deficits in cognitive performance. This was a distinct and better predictor of cognitive impairment than subjective and objective markers of homeostatic sleep pressure, as well as the pronounced thalamo-cortical connectivity changes that occurs towards falling asleep. The ratio of within vs between network integration in the cortex increased further in the NREM sleep, suggesting that prolonged wakefulness drives the cortex toward a state resembling sleep. Importantly, reversal of the balance between segregation and integration of cortical activity was related to both performance decline following SD, and recovery after the nap. Leveraging intra- and inter-individual differences in network integration and segregation may play a critical role in identifying vulnerability to cognitive impairment in the sleep deprived state.Significance StatementPaste your significance statement here. Please note that it should not exceed 120 words, but should be at least 50 words in length. It should not include any references.