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To determine the effect of extracorporeal pelvic floor magnetic stimulation in children with an overactive bladder, as although such stimulation is an effective treatment for voiding dysfunction such as urge incontinence (UI) and urgency-frequency syndrome, experience in children is scarce.This prospective study included 42 children diagnosed with an overactive bladder, based on urodynamic or video-urodynamic study; a complete follow-up was available in 34. The children were grouped into those with UI only, not monosymptomatic nocturnal enuresis (nMNE), or MNE, according to their symptoms. Clinical variables were assessed by recording a voiding and nocturnal enuresis diary before and after magnetic stimulation, the latter being administered twice a week for 4 weeks using a size-adjusted magnetic chair (each session took 20 min).The UI only and nMNE group had a significant decrease in voiding frequency and frequency of UI (P < 0.05); the MNE group also had a significant decrease in voiding frequency (P < 0.05). There was a significant increase in functional bladder capacity in all groups (P < 0.05) but no significant decrease in the mean volume and frequency of NE in the nMNE and MNE groups (P > 0.05).Extracorporeal pelvic floor magnetic stimulation has an acute effect on voiding dysfunction such as urge syndrome in children. However, controlled studies with a sham-stimulation group and various durations of stimulation are necessary for its application as a primary treatment for voiding dysfunction in children.