Purpose <p>This study aims to investigate the optimal surgical timing for symptomatic choledochal cyst (CDC) with hyperamylasemia in children.</p> Methods <p>We retrospectively reviewed 61 symptomatic CDC patients with hyperamylasemia who underwent cyst excision and Roux-en-Y hepaticojejunostomy between July 2020 and November 2021. Patients were either in symptomatic phase or in remission at the time of surgery.</p> Results <p>Thirty-seven patients were assigned to the symptomatic group and 24 to the remission group, with no significant difference in conversion rates (5.4% vs. 4.2%, <i>P</i> = 1.000). In the symptomatic group, two patients (5.4%) developed biliary fistulas, and two (5.4%) experienced pancreatitis. In the remission group, one patient (4.2%) had active bleeding, and one (4.2%) developed a biliary fistula without statistically significant difference (<i>P</i> = 1.000). The median total, preoperative, and postoperative hospital stays were comparable between the groups (<i>P</i> = 0.411, <i>P</i> = 0.159, and <i>P</i> = 0.731, respectively). However, costs were higher in the symptomatic group (<i>P</i> = 0.043). The two groups exhibited similar pathological inflammation severity (<i>P</i> = 0.065).</p> Conclusion <p>Postponing surgery until symptom remission demonstrates no therapeutic advantage for children with CDC and hyperamylasemia. Early surgery should be considered, provided that the general condition of the patient permits.</p>