Delirium is characterized by inattention and other cognitive deficits, symptoms that have been associated with disturbed interactions between remote brain regions. Recent EEG studies confirm that disturbed global network topology may underlie the syndrome, but lack an anatomical basis. The aim of this study was to increase our understanding of the global organization of functional connectivity during delirium and to localize possible alterations. Resting-state fMRI data from 44 subjects were analyzed, and motion-free data were available in nine delirious patients, seven post delirium patients and thirteen non-delirious clinical controls. We focused on the functional network backbones using the minimum spanning tree, which allows unbiased network comparisons. During delirium a longer diameter (mean (M) = 0.30, standard deviation (SD) = 0.05, P = .024) and a lower leaf fraction (M = 0.32, SD = 0.03, P = .027) was found compared to the control group (M = 0.28, SD = 0.04 respectively M = 0.35, SD = 0.03), suggesting reduced functional network integration and efficiency. Delirium duration was strongly related to loss of network hierarchy (rho = −0.92, P = .001). Connectivity strength was decreased in the post delirium group (M = 0.16, SD = 0.01) compared to the delirium group (M = 0.17, SD = 0.03, P = .024) and the control group (M = 0.19, SD = 0.02, P = .001). Permutation tests revealed a decreased degree of the right posterior cingulate cortex during delirium and complex regional alterations after delirium. These findings indicate that delirium reflects disintegration of functional interactions between remote brain areas and suggest long-term impact after the syndrome resolves.