Background. Functional dyspepsia is a common chronic disorder with non specific upper abdominal pain or discomfort. Different approaches with anti-secretory, spasmolytic, prokinetic and anti-inflammatory effects and most preferably reduction of visceral hypersensitivity seem logical. In this study, we compared the effectiveness of the four most drugs used for treatment of dyspepsia in children. Methods. 169 patients between 2 to 16 years old that 47.3% was male and 52.7% was female were enrolled in this clinical trial study by the diagnosis of functional dyspepsia. Then for each patient one of the drugs; Omeprazole, Famotidine, Ranitidine or Cimetidine was administered, for a period of 4 weeks. Patients were followed after 2 and 6 weeks from the beginning of the treatment. Results. The distribution of drugs between these patients were including; 21.9% with Cimetidine, 21.3% with Famotidine, 30.8% with Omeperazole and 26% with Ranitidine that the proportion of patients with all symptoms relief were: 21.6% for Cimetidine, 44.4% for Famotidine, 53.8% for Omeprazole and 43.2% for Cimetidine (P = .024). In followups within 2 and 6 weeks after beginning medical therapy, no side effects due to drugs were seen. Conclusion. If a cure is defined as all symptoms relief after a period of 4 weeks treatment, our findings showed that Omeperazole are superior to Ranitidine, Famotidine, and Cimetidine for management of functional dyspepsia.