Split notochord syndrome is a group of developmental abnormalities caused by abnormal splitting or deviation of the notochord, clinically resulting in the duplicated bowel associated with vertebral anomalies. In this syndrome, initial presentations due to duplicated bowel, vomiting, abdominal pain, and failure to thrive, usually occur before 1 year of age. We here report a 12-year-old boy with intermittent vomiting, previously diagnosed with cyclic vomiting syndrome. On abdominal x-ray examination, a defect in the closure of posterior vertebral arches was observed in the 5th lumbar vertebral body, indicating the complication of spina bifida occulta. This finding suggested the diagnosis of split notochord syndrome. A magnetic resonance imaging study revealed a cystic mass lesion in the pelvic cavity. ^99mTc-pertechnetate scintigraphy, which is frequently used to detect ectopic gastric mucosa for the diagnosis of Meckel's diverticulum, showed a positive spot corresponding to the cystic mass lesion. Surgical resection of the cystic mass lesion demonstrated ileal duplicaion with ectopic gastric mucosa. Surgical findings suggest that symptoms of the patient were due to ulceration, inflammation, or bleeding caused by acid-peptic juice secreted from ectopic gastric mucosa. Duplication of the alimentary tract should be considered as a possible cause in patients with symptoms suggesting cyclic vomiting syndrome.