Despite advancements in medical therapy for ulcerative colitis (UC), a significant proportion of children progress to colectomy with ileal pouch-anal anastomosis (IPAA). Procedural related complications between two- and three-stage operations in children have not been well described. We performed a retrospective review of patients who underwent a colectomy for UC or inflammatory bowel disease unclassified between 2008 and 2018. Forty-nine children underwent an IPAA at the time of colectomy (two stage) or during a subsequent operation (three stage). Preoperative hemoglobin and albumin concentrations were lower among those undergoing three-stage procedures. The rate of early complications (≤30days) was similar between the two groups (p = 0.46); however, late complications (>30days) were more commonly associated with three-stage procedures (p = 0.03). Time with a stoma was 3.2months longer among those who underwent a three-stage procedure. While three-stage procedures were more often performed during the first half of the study period (2008-2012), two-stage procedures became more common during the second half (2013-2018). During this transition to favor two-stage procedures, complication rates did not significantly change. Although three-stage procedures were thought to be associated with fewer complications, we found comparable complication rates as we transition to two-stage procedures.