Recurrent abdominal pain (RAP) in children is common, with most functional in origin. Colonoscopy has sometimes been performed to exclude pathology but its role is unclear. Our aim therefore was to assess the diagnostic yield and role of colonoscopy in these children. Retrospective review of consecutive colonoscopies in a tertiary pediatric hospital between November 2011 and October 2015 was undertaken. Only those with RAP as an indication for procedure were included. Chart review of patients with pain was undertaken to ensure they fulfilled Rome IV criteria. Patient demographics, indication for procedure, and adjunct preprocedure tests were noted. Statistical analyses were performed with SPSS software. A total of 652 colonoscopies were performed, of which 68 (10%) had abdominal pain as one of the indications, and was the sole indication in 15 (2%) patients. All 68 patients had preprocedure serum inflammatory markers measured and 53% (36/68) had stool calprotectin. Positive histology was found in 10% (7/68) including Crohn disease (n = 3), polyps (n = 2), and microscopic colitis (n = 2). The remaining 61 patients had normal colonoscopy and ileocolonic biopsies. Of the 36 patients 5 had raised fecal calprotectin, and all had abnormal histology. Serum inflammatory markers were raised in 4 patients and all also had abnormal calprotectin. No patient with isolated abdominal pain had positive histology. Rectal bleeding was the only associated indication to predict abnormal histology (P = 0.019). Colonoscopy is likely not warranted in children with RAP without bleeding, weight loss, or altered bowel habit. Fecal calprotectin is useful in helping predict positive findings.