Abstract Background Functional dyspepsia (FD) is a constellation of diverse gastrointestinal disturbing symptoms with multifactorial feature, that are not attributable to organic causes after proper medical assessment. Treatment options are unsatisfactory due to the lack of identifiable pathophysiology as well as the pharmacological therapy are less effective, so using an additional reliable non- pharmacological therapy would be promising. Bee honey has been used as a complementary and alternative medicine for its several benefits in different health aspects. Objective To assess the effect of bee honey as an adjuvant therapy among children with functional dyspepsia. Patients and Methods In this randomized controlled clinical trial (RCT) 30 patients aged (8-18) years old according to Rome IV criteria from Gastroenterology Clinic in Children’s Hospital, Ain Shams University, Egypt. Patients were randomly allocated into 2 groups; both groups received proton pump inhibitor (PPI) for 4 weeks and the intervention group received honey in addition. Both groups were re-assessed after this period. All patients were subjected to thorough history taking, physical examination and follow-up assessment which was done every week during the study period. Assessment of the severity of dyspepsia was done by using "Modified Glasgow Dyspepsia Severity Score" (MGDS) score. Results There were no significant differences in the baseline sociodemographic characteristics and total scores at the beginning of the study among both groups(p > 0.05). A significant beneficial effect of honey combined with PPI in improvement of FD and decrease severity of symptoms in intervention group which was evident from significant decreases in total score interpretation (P < 0.05). There was statistically significant difference between both groups as regards to the percentage of improvement, where the patients who received honey showed a higher percentage of cure rate (P < 0.05). Conclusion Honey supplementation combined with PPI could be used as a novel therapeutic modality in children with functional dyspepsia with high cure rate.