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Recently, functional near-infrared spectroscopy (fNIRS) has been utilized to image the hemodynamic activities and connectivity in the human brain. With the advantage of economic efficiency, portability, and fewer physical constraints, fNIRS enables studying of the human brain at versatile environment and various body positions, including at bed side and during exercise, which complements the use of functional magnetic resonance imaging (fMRI). However, like fMRI, fNIRS imaging can be influenced by the presence of a strong global component. Yet, the nature of the global signal in fNIRS has not been established. In this study, we investigated the relationship between fNIRS global signal and electroencephalogram (EEG) vigilance using simultaneous recordings in resting healthy subjects in high-density and whole-head montage. In Experiment 1, data were acquired at supine, sitting, and standing positions. Results found that the factor of body positions significantly affected the amplitude of the resting-state fNIRS global signal, prominently in the frequency range of 0.05–0.1 Hz but not in the very low frequency range of less than 0.05 Hz. As a control, the task-induced fNIRS or EEG responses to auditory stimuli did not differ across body positions. However, EEG vigilance plays a modulatory role in the fNIRS signals in the frequency range of less than 0.05 Hz: resting-state sessions of low EEG vigilance measures are associated with high amplitudes of fNIRS global signals. Moreover, in Experiment 2, we further examined the epoch-to-epoch fluctuations in concurrent fNIRS and EEG data acquired from a separate group of subjects and found a negative temporal correlation between EEG vigilance measures and fNIRS global signal amplitudes. Our study for the first time revealed that vigilance as a neurophysiological factor modulates the resting-state dynamics of fNIRS, which have important implications for understanding and processing the noises in fNIRS signals.