Purpose We aimed to describe our robotic-assisted surgery (RAS) techniques and assess the early results of RAS for choledochal cysts in children. Methods We conducted a retrospective chart review of children who underwent RAS for a congenital choledochal cyst at our institution between February 2013 and August 2016. We analyzed patient characteristics, operative data, and postoperative outcomes. Results Thirty-nine patients underwent RAS for a choledochal cyst (female 30). The operation was performed with four robotic ports and one laparoscopic port for the assistant. The Roux loop was fashioned extracorporeally. Twenty patients (51.3%) had a Todani Type I cyst and the others had Type IV. The mean patient age and weight and choledochal cyst diameter at the time of the operation were 40.2 months (range 5–108 months), 13.4 kg (range 6.5–29 kg), and 27.2 mm (range 9–112 mm), respectively. The mean operating time was 192.7 min (range 150–330 min). There were no intraoperative complications; no conversions to laparoscopic or open surgery; and no postoperative complications, including cholangitis, cholelithiasis, or anastomotic stenosis. Conclusion Pediatric RAS CC resection is safe and feasible. The robot-assisted technique overcame technical difficulties. However, in pediatric cases, a skilled robotic surgical team and procedural modifications are needed.