Background In this study, the biliary-enteric anastomosis following choledochal cyst excision was studied using continuous suture and interrupted suture procedures in a pediatric population. Patients and methods In this study, information on 57 children who received continuous suture choledochal cyst surgery at our facility between 2015 and 2020 was gathered retrospectively. The patients that were enrolled were divided into two groups: continuous suture ( n =24) and interrupted suture ( n =33). Anastomotic leakage, anastomotic duration in minutes, hospital stay in days, and cost were all compared between these groups. Results The incidence of anastomotic leakage was higher in the interrupted suture group (4.17 vs. 6.6% for continuous suture and interrupted suture, respectively), but the difference was statistically insignificant ( P =0.63). The groups did not differ regarding hospital stays ( P =0.25). The mean time required to complete the anastomosis in the continuous suture group was 15.3±4.1 min, compared with 23.5±5.2 min in the interrupted suture group ( P <0.0001). The costs were &z.euro;5±0.0 in the continuous suture group and &z.euro;30±6.4 in the interrupted suture group ( P <0.0001). Conclusion The anastomotic leakage and hospital stay did not differ between the continuous suture and interrupted suture groups. In contrast, the continuous suture group had a considerable advantage over the interrupted suture group in terms of anastomotic duration and cost.