Laparoscopic surgery (LS) for choledochal cyst (CC) is now performed at many institutions. This study aimed to compare LS and open surgery (OS) for CC in children based on multicenter study at all institutions in Kyushu, Japan. A regional multicenter study was conducted among institutions affiliated with Kyushu Pediatric Surgery Study Group. Kyushu is located in the southern region of Japan, where approximately 10 % of the population live. Patients with CC who underwent definitive surgery between 2014 and 2023 were enrolled in this study. Patients' backgrounds, operative results, and postoperative complications were investigated. All 28 affiliated institutions joined the study. There were 231 cases, including 75 (32.5 %) cases treated with LS and 154 (67.5 %) treated with OS. In comparison to with OS, LS was associated with a significantly higher rate of preoperative cholangitis (LS: 61.3 % vs. OS: 40.4 %, p < 0.01) and lower rate of preoperative bile duct perforation (LS: 0.0 % vs. OS: 6.4 %, p = 0.025). LS had a significantly longer operative time (LS: 511.0 min vs. OS: 376.8 min, p < 0.01) and lower blood loss than OS. Hepaticojejunostomy was performed in all patients with LS and 98.7 % of patients with OS. There were no significant differences in postoperative complications during hospitalization between the 2 groups. Regarding late postoperative complications, anastomotic stenosis tended to be more common in the LS group, but the difference was not statistically significant (LS: 6.7 % vs. OS: 2.0 %, p = 0.065). The clinical outcomes of LS for CC were comparable to those of OS.