The perception of pain in children is easily influenced by environmental factors and psychological comorbidities that are known to play an important role in its origin and response to therapy. Chronic abdominal pain is one of the most commonly treated conditions in modern pediatric gastroenterology and is the hallmark of 'functional' disorders that include irritable bowel syndrome, functional dyspepsia, and functional abdominal pain. The development of pharmacological therapies for these disorders in adults and children has been limited by the lack of understanding of the putative, pathophysiological mechanisms that underlie them. Peripheral and central pain-signaling mechanisms are known to be involved in chronic pain originating from the gastrointestinal tract, but few therapies have been developed to target specific pathways or enhance correction of the underlying pathophysiology. The responses to therapy have been variable, potentially reflecting the heterogeneity of the disorders for which they are used. Only a few small, randomized clinical trials have evaluated the benefit of pain medications for chronic abdominal pain in children and thus, the decision on the most appropriate treatment is often based on adult studies and empirical data. This review discusses the most common, non-narcotic pharmacological treatments for chronic abdominal pain in children and includes a thorough review of the literature to support or refute their use. Because of the dearth of pediatric studies, the focus is on pharmacological and alternative therapies where there is sufficient evidence of benefit in either adults or children with chronic abdominal pain.