Background: Hirschsprung disease (HD) is associated with substantial postoperative morbidity, particularly due to Hirschsprung-associated enterocolitis (HAEC), despite definitive surgical treatment. Postoperative outcomes may vary according to the length of the aganglionic segment and the surgical technique used, and optimal management of recurrent HAEC remains a significant clinical challenge. Methods: The medical records of patients who underwent corrective surgery for HD between 2011 and 2023 were retrospectively reviewed. Demographic characteristics, disease segment length, surgical technique, postoperative complications, and HAEC episodes were recorded. HAEC diagnosis and follow-up assessments were conducted in accordance with the Delphi criteria. Patients with recurrent HAEC and obstructive symptoms refractory to standard conservative management were evaluated for botulinum toxin injection (BTI). Results: A total of 72 patients were included in the study. The majority of the patients were male (83.3%), with a mean age at diagnosis of 11 months. The Duhamel procedure was the most frequently performed surgical technique. Although the rate of anastomotic leakage was greater in patients who underwent the Swenson procedure compared with the Duhamel group, this difference did not reach statistical significance when the appropriate statistical methods were used because the small sample size. No significant difference in the incidence of HAEC was observed among the different surgical techniques. BTI was administered to 13 patients, and regression of enterocolitis episodes according to the Delphi criteria was observed in 11 patients (84.6%). Most postoperative complications are observed in patients with long-segment Hirschsprung disease. Conclusions: Postoperative complications and HAEC remain major clinical challenges in the management of Hirschsprung disease, particularly in patients with long-segment involvement. Although the surgical technique may influence certain complication rates, HAEC appears to be a multifactorial condition. Botulinum toxin injection may serve as a supportive treatment option in selected patients with refractory HAEC; however, prospective controlled studies are needed to further clarify its role.