Abstract Background Reoperation for total colonic aganglionosis (TCA) may be required for residual aganglionosis after an initial radical operation. We aimed to investigate the symptoms, management, and outcomes of patients who required a redo pull-through (Redo PT). Methods Nine TCA patients underwent Redo PT at our center between 2007 and 2017. Their medical records were reviewed. Parental telephone interviews that included disease-specific clinical outcomes were conducted, and post-operative complications and long-term outcomes (including height-for-age/weight-for-age and bowel-function score) were compared to those of single-pull-through (Single PT) patients (n = 21). Results All the nine Redo PT patients suffered obstruction within 1 month after the initial operation that could not be alleviated by conservative treatment. All abdominal X-ray/contrast barium enemas showed proximal bowel dilatation, indicating residual aganglionosis. The median ages at the initial operation and Redo PT were 200 and 509 days, respectively. Reoperation consisted of an intraoperative frozen biopsy and a modified laparotomic Soave procedure in all patients. Post-operative complications included perianal excoriation (n = 3), intestinal obstruction (n = 2), enterocolitis (n = 2), and rectovestibular fistula (n = 1). Seven Redo PT patients were followed up for a mean time of 7.1 ± 2.3 years; six (85.7%) had good growth and four (57.1%) had good bowel-function recovery. Post-operative complications and long-term outcomes were almost equal between the Redo PT and Single PT groups (all P > 0.05). Conclusion TCA patients with recurrent obstructive symptoms and dilated proximal bowel may have residual aganglionosis after an initial operation. Redo PT is effective and provides good long-term outcomes comparable to those of patients who benefited from Single PT.