To determine the characteristics of brain development in children with nocturnal enuresis, we investigated the intensity of functional connectivity both among the nodes in the brain network and between the two hemispheres of the brain. Twenty-three children with nocturnal enuresis (NE) and an equal number of normal children were examined using resting-state functional magnetic resonance imaging (fMRI) scans. Data analysis was done via the degree centrality (DC) and voxel-mirrored homotopic connectivity (VMHC) approaches. Moreover, we compared the children's psychological status by utilizing the self-concept scale. In four areas of the brain, the the DC values of the NE group were obviously lower than that of the normal controls. These four areas were the posterior cerebellar lobe, anterior cingulate cortex (ACC), medial frontal gyrus, and superior left temporal gyrus (P < 0.05, after correction). We also found two brain areas where the VMHC values of the NE group were obviously lower than that of the normal controls. The two groups were the cerebellar lobe and the anterior cingulate cortex (ACC) [P < 0.05, after correction]. A psychological comparison between the children with NE and that in the normal group on the self-concept scale was also performed. The scores of the children with NE were lower than normal controls regarding behavior, appearance and property, anxiety, gregariousness, happiness, and satisfaction (P < 0.05). These findings provide evidence of the deficit of urination control in children with NE. Furthermore, through the methods of DC and VMHC, which are based on functional connectivity, it was also possible to explain why children with NE often have the concomitant symptoms of attention, control, and memory problems. The analysis of the self-concept scale suggests that children with NE lack self-confidence.