The two most commonly performed methods of biliary-enteric reconstruction following choledochal cyst resection are Roux-en-Y hepaticojejunostomy (HJ) and hepaticoduodenostomy (HD). There is a lack of consensus regarding the better technique between them. This study aimed to evaluate the outcomes, efficacy and early complications of HD as a mode of biliary reconstruction after surgical resection of a choledochal cyst. This was a multi-institutional prospective study carried out in high-volume tertiary care teaching institutes from January 2010 to December 2022. All children managed with HD following choledochal cyst resection were analysed for their early complications and outcomes. A total of 74 patients were included in this study. There were 59 (79.73%) females and 15 (20.27%) males. Thirty-nine (52.70%) patients had jaundice at the time of presentation. Magnetic resonance cholangiopancreatography was performed in 57 (77.03%) patients following ultrasonography. Intraoperatively, malrotation was present in 2 (2.70%) patients. In our study, operating time ranged from 60 to 195 min (mean: 118 min). Hospital stays ranged from 8 to 17 days (mean: 11.5 days). The post-operative biliary leak was seen in 7 (9.50%) patients, out of which 6 (8.11%) minor leaks were managed conservatively. Roux-en-Y HJ was performed on 1 (1.35%) patient with a major leak. In our series, 4 (5.40%) patients developed cholangitis; post-operative haemorrhagic nasogastric aspirate 5 (6.76%), post-operative pancreatitis 3 (4.05%) and wound infection 4 (5.40%) were observed and managed conservatively. None of the patients in our study developed an anastomotic stricture, bile gastritis and adhesive small bowel obstruction. Resection of choledochal cyst with HD reconstruction is safe and feasible with short operative time. HD is a viable option for operative management of choledochal cyst with low complication rates and faster recovery.