At the present time, it is nearly impossible to treat pediatric functional gastrointestinal disorders associated with pain in an evidence based fashion. This is due to the overall lack of controlled studies and, even more importantly, the complexity of the contributors to disease phenotype which are not controlled or accounted for in most therapeutic trials. In this manuscript, we review the challenges of defining entry criteria, controlling for the large number of biopsychosocial factors which may effect outcomes, and understanding pharmacokinetic and pharmacodynamic factors when designing therapeutic trials for abdominal pain in children. We also review the current state of pediatric abdominal pain therapeutics and discuss trial design considerations as we move forward.