Introduction: Choledochal cyst (CC) is a rare congenital malformation of biliary tract. There occurs pathological dilatation of extrahepatic and/or intrahepatic biliary tree. About 85% of cases are reported below 15 years of age. Excision of choledochal cyst is required to relieve biliary obstruction thereby protecting the liver and pancreas as well as to prevent malignancy in long term. But controversy persists in the two existing techniques of biliary reconstruction after cyst excision. Objective: To analyze the clinical presentation, incidence and types of choledochal cyst and our experience in management of these congenital anomalies and compare the advantages and disadvantages between two modalities of biliary reconstruction. Methods: A prospective, controlled, clinical trial was conducted on patients with choledochal cyst in the Department of Pediatric Surgery, Sir Salimullah Medical College & Mitford Hospital, Dhaka, Bangladesh. They were divided into two groups; Group–A: Patients in whom biliary reconstruction was done by Roux-en-Y hepaticojejunostomy, Group-B: Biliary reconstruction done by Hepaticoduodenostomy. The two groups were compared in respect to clinical course, types of cyst, surgical difficulties with special emphasis on operating time, postoperative complications. Results: Choledochal cysts accounted for 0.79% of total admissions at our institute. Out of 31 admitted cases, 22 cases were enrolled in the study. The number of patients in group A was 10 and in group B were 12. Abdominal pain was the commonest presenting feature and Type I choledochal cyst was the most common finding. The average duration of surgery was less in group B (1 hour 25 min) than in group a (2 hours and 10 min). Conclusion: Biliary reconstruction by Hepaticoduodenostomy takes significantly less operative time than Roux-en-Y hepaticojejunostomy (p<0.05) and needs single anastomosis. It is more anatomical, physiological, and easy to perform and associated with fewer complications.