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Objectives Dynamic perineal ultrasonography to assess the function of the pelvic floor muscles in children with micturition complaints shows that many children with daytime incontinence or recurrent urinary tract infections use their pelvic floor paradoxically. They strain when asked to withhold urine, or they have no voluntary control of the pelvic floor muscles at all. The aim of this study was to record the pelvic floor function and evaluate the physical therapy regimens for children with dysfunctional voiding (DV) and paradoxical pelvic floor function. Methods A total of 65 patients with DV, many who also had constipation, were diagnosed with paradoxical movement of the pelvic floor. The patients were asked to contract their pelvic floor muscles during a perineal dynamic ultrasound investigation. Of the 52 patients treated by physical therapists, 32 had a single 1-hour biofeedback session with rectal examination and anal balloon expulsion. In the remaining 20 patients, this was followed by 2 weeks of biofeedback balloon expulsion training at home. Forty control patients were observed. Results In 13 of the 65 patients, the diagnosis could not be confirmed by the physical therapists. At 6 to 10 months after training, 50 of the 52 other patients had normal voluntary pelvic floor muscle control. Of the 40 control patients, 39 had normal pelvic floor control. Conclusions The results of this study have demonstrated that pelvic floor dysfunction occurs frequently in children with DV and can be cured by dedicated physical therapy. The clinical importance of this phenomenon is not yet clear. Prospective studies will teach us more about the true incidence and therapeutic effect of pelvic floor dysfunction on DV.