Objective: Treating voiding dysfunction without anatomical obstructions is challenging. Urethral onabotulinum toxin A (BoNT-A) is used in treating voiding dysfunction; however, the success rate varies widely, and patients may not be satisfied with the treatment outcome. This study compared the efficacy of the urethral BoNT-A injection between patients with different non-spinal cord injury (SCI) voiding dysfunctions. Materials and Methods: This study retrospectively analyzed patients with refractory voiding dysfunction, including detrusor underactivity (DU), dysfunctional voiding (DV), and poor relaxation of the external sphincter (PRES) who received the urethral sphincter 100 U BoNT-A injection. The treatment outcomes were assessed via a global response assessment (GRA) one month after treatment. Baseline and follow-up videourodynamic study (VUDS) parameters were also compared. Results: Totally, 161 patients (60 with DU, 77 with DV, and 24 with PRES) with a mean age of 58.8 ± 20.2 were enrolled, of which 62.1% had a good response (GRA ≥ 2) after urethral BoNT-A injection. DV patients had a higher success rate (76.6%) than DU (50%) and PRES (45.8%) patients (p = 0.002). A diagnosis of DV, higher voided volume and recurrent urinary tract infection were predictors of a good treatment response, while the cervical cancer status post-radical surgery predicted a poor response. Receiver operating characteristic (ROC) curve analyses identified PVR >250 mL as a negative predictor (p = 0.008) in DU patients. Conclusions: The urethral BoNT-A injection provides a satisfactory success rate for non-SCI voiding dysfunction. Patients with DV benefit most from both subjective and objective parameters. Approximately 50% of patients with DU and PRES also had a fair response. PVR > 250 mL was a negative predictor in DU patients.