Sleep deprivation is an important cause of cognitive impairment, and anterior insular subregions are core brain regions linked to cognitive function. However, the relationship between anterior insular subregions functional connectivity (FC) and the cognitive impairment that occurs following total sleep deprivation (TSD) remains unknown. As such, this study was designed to evaluate how such anterior insular subregions FC alterations are linked with impaired cognitive activity after TSD. This study recruited 20 healthy volunteers who underwent two rounds of resting-state functional magnetic resonance imaging (rs-fMRI), with one being conducted while in a state of rested wakefulness (RW) and the other being conducted following 24 h of TSD. These rs-fMRI data were then used to conduct seed-based FC analyses for the bilateral anterior insular subregions, including the dorsal anterior insula (dAI) and the ventral anterior insula (vAI). The Psychomotor Vigilance Test (PVT) was used to gauge cognitive performance, and associations between altered FC in these anterior insular subregions and PVT performance following TSD were measured using Pearson correlation analyses. Significant changes in the FC of these bilateral insular subregions were observed following 24 h of TSD relative to the RW state. Significantly enhanced FC was evident between the left dAI and right superior frontal gyrus (SFG), right dAI and bilateral SFG and right putamen, and right vAI and left medial SFG. Moreover, the observed enhancement of FC between the left vAI and right SFG functional connectivity was positively correlated with worse PVT performance. These data suggest that altered FC in the anterior insular subregions represents a prominent neuroimaging biomarker associated with cognitive impairment following TSD.