Functional abdominal pain (FAP) causes disruption of daily activities/missed school days, over utilization of healthcare, unnecessary surgeries, and anxiety in 10-15% of children. Its etiology is not clearly understood, however the success of several clinical protocols suggests that autonomic dysregulation is a factor. In this study autonomic activity, including heart rate variability (HRV), was compared between children with FAP and a comparison group. Twenty children with FAP and 10 children without FAP between the ages of 5 and 17 years old were compared on autonomic regulation using an ambulatory system at baseline and 8 weeks later. Children with FAP participated in 6 sessions of HRV biofeedback aimed at normalizing autonomic balance. At baseline, children with FAP appear to have more autonomic dysregulation than children without FAP. After completing HRV biofeedback, the FAP group was able to significantly reduce their symptoms in relation to significantly increasing their autonomic balance. In a sample of children with FAP, it appears that HRV biofeedback treatment improved their symptoms and that a change in vagal tone was a potential mediator for this improvement. The present study appears to point to excessive vagal withdrawal as an underlying mechanism of FAP.