Background: The operative duration might be important for perioperative morbidity and the involvement has not been fully characterized in pediatric patients. We here determined the perioperative variables in association with operative duration and its influence on the clinical outcome in the pediatric patients.Methods: We retrospectively reviewed 701 patients who underwent elective choledochal cysts followed by Roux-en-Y hepaticojejunostomy between August 2010 and Aug 2019. Based on the median operating time (165 min), patients were separated into two groups, including a long-time group (>165 min) and a short-time group (<165 min). The independent risk factors for the operative time were determined usng the multivariable logistic regression analyses. To adjust for any potential selection bios, propensity score matching was performed for the long-time and short-time groups. In the 192 matched patients, perioperative outcomes, including postoperative recovery, complications measurement, and length of hospital stay were analyzed.Results: The operating time was often increased by excision difficulty caused by the lager choledochal cyst size (OR=1.56; 95% CI, 1.09-2.23; p<0.001), the greater BMI(OR=1.02; 95% CI, 1.00-1.15; p=0.018), older age (OR=1.17; 95% CI, 1.02-1.39; p=0.012) under multivariate analysis. The long-time surgical duration was associated with delay for gastrointestinal functional recovery, measured with the first defecation (p=0.027) and first bowel movement (p=0.019). Moreover, a significant decrease in serum albumin were presented in the long-time group compared with the short time group (p=0.0035). The total length of postoperative hospital stay was longer in patients with long-time group (7.51±2.03 days) than patients with short-time group (6.72±1.54 days, p = 0.006).Conclusions: Our data demonstrated that short operating time was associated with favorable postoperative results. The influencing factors for operating time could be ameliorated in the perioperative period to gain a better outcome after major abdominal operations.