The mechanism underlying the alteration of neural activity in the human brain and the vigilance level during sleep deprivation (SD) remains a subject of ongoing investigation, particularly with regard to the sensorimotor and visual systems. Resting-state functional magnetic resonance imaging (rfMRI), a noninvasive imaging technology reflecting spontaneous activity of the human brain, is widely used in SD research. In the present study, nine repeated rfMRI sessions followed by a psychomotor vigilance task (PVT) were used to explore the alteration of neural activity and vigilance level during 36 h of SD in 23 volunteers. Mean reaction time (MRT) and lapse ratio (LR) based on PVT were measured to assess variation in vigilance level. The sensorimotor network (SMN) and visual network (VN) are the most vulnerable areas after obtaining SD measures from ReHo (regional homogeneity) and ALFF (amplitude of low-frequency fluctuation) based on rfMRI. Group-ICA was used to parcellate the visual-related regions into visual area Ⅰ, visual area Ⅱ, and the visual association area. Sensorimotor-related regions, including the bilateral precentral/postcentral gyrus, the bilateral paracentral lobule, and the supplementary motor area (SMA), were extracted from the anatomical automatic labeling (AAL) templates. Brain neural activity and vigilance level were deteriorated at 16-30 h of SD. A 2 × 3 repeated-measures ANOVA was used to explore the effects of sleep pressure and circadian rhythm and their interaction on neural activities of sensorimotor-related and visual-related regions. Significant effects of sleep pressure and interaction on all sensorimotor-related and visual-related regions were observed. Pearson’s correlation coefficients were used to explore the relationships between variation in vigilance level and alteration in brain neural activities of sensorimotor-related and visual-related regions. Significant correlations were observed between the neural activities of all sensorimotor-related regions and variation in vigilance during SD. Our results confirmed that SD alters the vigilance level and neural activity of the SMN and the VN, beginning at 24:00 on the first day, and sleep pressure and circadian rhythm regulate the neural activity of the SMN and VN during SD. Furthermore, sleep pressure significantly regulates the effects of circadian rhythm. The enhancement of ReHo in the SMN and VN leads to a weakening of their remote connections, which may be the cause of the slowing of response time during SD.