Background/Objective: Hirschsprung-associated enterocolitis (HAEC) can occur before and after surgery, increasing the complication rates, hospital stay, and treatment costs. This study aims to determine the incidence of preoperative and postoperative Hirschsprung-associated enterocolitis HAEC and the related risk factors. Methods: This study is a prospective cohort study of Hirschsprung’s disease patients under 16 years of age at two Children’s Hospitals in Ho Chi Minh City, Vietnam from December 2022 to June 2024. The postoperative follow-up is 12 months. Results: We enrolled 84 pediatric patients, with a male-to-female ratio of 5.4/1 and an average age of 7.2 ± 1.07 months. Of the patients, 25% had preoperative enterocolitis at the time of admission. Statistical analysis revealed that risk factors for preoperative enterocolitis at admission included a history of enterocolitis (p = 0.024), low weight in hospital (p = 0.001), and lack of preoperative treatment (p = 0.01). Postoperative enterocolitis occurred in 14 patients (16.7%) at an average of 4.03 months postoperatively. Multiple logistic regression of postoperative enterocolitis was associated with a history of preoperative enterocolitis (p < 0.001), anastomotic stricture (p = 0.002), and the length of the aganglionic segment (p = 0.031). No statistically significant association was found between the surgical method and the risk of postoperative enterocolitis. Conclusions: A history of preoperative enterocolitis, low weight, and anastomotic stricture are significant risk factors for postoperative enterocolitis in patients with Hirschsprung’s disease. Therefore, preoperative medical treatment is recommended for the patients who have not yet undergone a definitive surgical procedure.