Over the last 15 years, the laparoscopic-assisted endorectal pull-through procedure has become the standard treatment for Hirschsprung disease in many centers around the world. Recently, single-incision laparoscopic techniques have drawn more attention. We describe a single-incision laparoscopic surgery (SILS) subtotal colectomy to treat long-segment Hirschsprung disease (LSHD) and Hirschsprung disease allied disorder (HAD) in children. A total of 22 patients who underwent SILS subtotal colectomy, including three patients with a failed first surgery, were included in this retrospective study. For SILS, a 1-cm skin incision was first made below the umbilical margin and a 5-mm trocar was placed into the abdomen after incising the peritoneum. Two 5-mm trocars were then placed on both sides of the umbilicus. Subsequently, based upon preoperative examination and biopsy results, we performed subtotal colectomy. The affected colon was mobilized successively beyond the peritoneum using high-frequency cutting and sealing devices, followed by a pull-through procedure and colon-anal anastomosis. The average operative time was 206.39 min. No case needed conversion from SILS to either conventional laparoscopy or open surgery. Of the 22 patients, 15 were diagnosed as LSHD, while 6 cases were diagnosed with intestinal neuronal dysplasia and one was diagnosed with hypoganglionosis. There were no intra-operative complications. One child had incision dehiscence on postoperative day three. During the follow-up over 12 months, all patients were noted to have excellent cosmetic outcomes, and enterocolitis was observed in four children. Subtotal colectomy with the SILS technique can be safely performed in LSHD or HAD patients in the pediatric population without major complications.