Sleep deprivation (SD) is very common in modern society and has a profound effect on cognitive function, in particular on working memory (WM). This type of memory is required for completion of many tasks and is adversely affected by SD. However, the cognitive neural mechanism by which SD affects WM, remains unclear. In this study, we investigated the changes in the brain network involved in WM after SD. Twenty-two healthy subjects underwent functional magnetic resonance imaging scan while in a state of resting wakefulness and again after 36 h of total SD and performed a WM task before each scanning session. Nineteen main nodes of the default mode network (DMN), dorsal attention network (DAN), fronto-parietal network (FPN), salience network (SN), and other networks were selected for functional analysis of brain network connections. Functional connectivity measures were computed between seed areas for region of interest (ROI)-to-ROI analysis and to identify patterns of ROI-to-ROI connectivity. The relationship between the significant changes in functional connectivity in the brain network and WM performance were then examined by Pearson's correlation analysis. WM performance declined significantly after SD. Compared with the awake state, the functional connectivity between DAN and DMN significantly increased after SD while that between FPN and DMN significantly decreased. Correlation analysis showed that the enhanced functional connectivity between DAN and DMN was negatively correlated with the decline in WM performance and that the decline in functional connectivity between FPN and DMN was positively correlated with decreased WM performance. These findings suggested that SD may affect WM by altering the functional connectivity among DMN, DAN, and FPN.