Purpose Nocturnal enuresis is a condition of intermittent incontinence during sleep in children. Previous studies have suggested that the abnormal brain function in enuresis should be investigated on the whole-brain network scale. This study aimed to investigate potential abnormalities in brain networks using resting-state functional magnetic resonance imaging data from 33 primary nocturnal enuresis patients and 34 healthy controls. Methods The functional components of brain networks were separated by spatial independent component analysis, followed by functional network connectivity analysis to explore the strength of the connections between the network components. In addition, correlations between the connectivity and behavior data were calculated. Results The enuresis children showed reduced inter-network connectivity among the default mode network, attention network, visual network, and sensorimotor network. Most of these connectivity measures were related to the bedwetting frequency or the cognitive performance. Conclusion Those alterations associated with improper attention allocation and poor cognitive-sensory integration may lead to bladder control dysfunction.