Objectives: Synchronous electroencephalogram (EEG) and functional magnetic resonance imaging (fMRI) has been used to explore sleep stage dependent functional brain networks. Despite a growing number of sleep studies using EEG-fMRI, few stud- ies have conducted network analysis on whole night sleep due to dif culty in data acquisition, artifacts, and sleep management within the MRI scanner. Methods: In order to perform network analysis for whole night sleep, we proposed experimental procedures and data process- ing techniques for EEG-fMRI. We acquired 6-7 hours of EEG-fMRI data per participant and conducted signal processing to re- duce artifacts in both EEG and fMRI. We then generated a functional brain atlas with 68 brain regions using independent com- ponent analysis of sleep fMRI data. Using this functional atlas, we constructed sleep level dependent functional brain networks. Results: When we evaluated functional connectivity distribution, sleep showed signi cantly reduced functional connectivity for the whole brain compared to that during wakefulness. REM sleep showed statistically different connectivity patterns compared to non-REM sleep in sleep-related subcortical brain circuits. Conclusion: This study suggests the feasibility of exploring functional brain networks using sleep EEG-fMRI for whole night sleep via appropriate experimental procedures and signal processing techniques for fMRI and EEG.