This study was to investigate the potential disturbance in cognitive control in enuretic children using functional MRI. Two groups including enuretic and healthy children were scanned during a color-word Stroop task to evaluate their task performance and neural response. Compared to the healthy subjects, the children with enuresis showed stronger Stroop effect and increased activation for the incongruent > congruent condition contrast in the anterior cingulate and the precentral/postcentral gyri. Our results suggested that the enuretic children showed altered neural responses to conflict events and tended to compensate by greater activation to sustain normal cognitive control.