Dysfunctional voiding (DV) is an abnormal urethral sphincter activity during voiding in neurologically normal individuals. Urethral sphincter botulinum toxin A (BoNT-A) injection has been used to treat DV, but the results have not been completely satisfactory. This study investigated the neurological characteristics of women with DV using the lower urinary tract electrophysiology (EP) study and the therapeutic efficacy of BoNT-A injection. In total, 48 women with DV and 16 women with normal voiding were included. Videourodynamic studies were conducted to diagnose DV before BoNT-A injection. EP studies, including urethral sphincter electromyography, bulbocavernosus reflex, and pudendal nerve conduction velocity, were conducted. Polyphasic motor unit action potentials suggestive of reinnervation were detected in 58.3% of patients with DV and 18.8% of controls (p = 0.001). Significant improvement in the corrected maximum flow rate (cQmax) was observed in patients with reinnervation at 1 and 3 months after BoNT-A injections into the urethral sphincter. Urethral sphincter denervation or reinnervation activity was commonly noted in 62.5% of women with DV. Repeated BoNT-A injections into the urethral sphincter provided effective treatment in 47.9% of patients, with mild improvement in cQmax observed in patients with urethral sphincter reinnervation. However, the improvement was not superior to those without reinnervation.