The purpose of this study was to assess cost variability in the care of abdominal pain-associated functional gastrointestinal disorders (AP-FGIDS) in youth across health systems, races, and specific AP-FGID diagnoses. Patients, aged 8–17 years, with a priority 1 diagnosis corresponding to a Rome IV defined AP-FGID were identified within the Health Facts® database. Total costs were obtained across the continuum of care including outpatient clinics, emergency department, and inpatient or observation units. Cost variability was described comparing different health systems, races, and diagnoses. Thirteen thousand two hundred and fourteen patients were identified accounting for 17,287 encounters. Total costs were available for 38.7% of the encounters. There was considerable variability in costs within and, especially, across health systems. Costs also varied across race, urban vs. rural site of care, and AP-FGID diagnoses. In conclusion, there was considerable variability in the costs for care of AP-FGIDs which is sufficient to support multi-site studies to understand the value of specific tests and treatments. Significant differences in costs by race merit further investigation to understand key drivers.