In patients who don’t respond to medical treatment, surgical procedures including colectomy and ileal pouch-anal anastomosis (IPAA), also known as J-pouch, are often indicated; however, pouchitis can develop in 80% of patients after the surgery and it may significantly impair quality of life. Recent studies have shown that IPAA without temporary ileal diversion has a relatively low complication rate, a low rate of small bowel obstruction, and provides excellent fecal control. A precise method for evaluating the clinical benefits associated with each procedure is lacking. The aim of this systematic review protocol is to outline how we will compare the clinical advantages or disadvantages of colectomy and J-pouch without ileostomy as opposed to with ileostomy. Our systematic review will identify retrospective and prospective cohort studies, case-control studies, and randomized-control trials where clinical outcomes such as postoperative complications and recurrence of colectomy and J-pouch with and without ileostomy are described. Secondary research (e.g., editorials, letters to the editor), case studies, and articles not written in English or French will be excluded. The following databases were searched on November 11th 2019: CINAHL (1982 onwards), CENTRAL, EMBASE (1980 onwards), and MEDLINE (1996 onwards). The following information will be obtained: citation details (title of the article and the year of publication); study details including study design; location of the study and its sample size; disease status, comorbidities, average or median follow-up, surgical details including the procedure implemented, and clinical outcomes such as frequency of small bowel obstruction, pouchitis, and recurrence. Observational studies will be assessed using the MINORS 2015 checklist. Statistical heterogeneity of the included studies will be assessed using the I-squared test with 95% confidence intervals, and publication bias will be determined using a funnel plot and Egger’s test when possible (>10 included studies). If a meta-analysis will be undertaken, the strength of the body of evidence will be assessed using GRADE. Examining the postoperative complications and clinical outcomes in children who undergo a J-pouch with ileostomy versus without ileostomy will aid clinical practitioners, particularly surgeons, in addressing the optimal surgery type for managing children with inflammatory diseases to minimize their post-operative discomfort and recurrence.