There is an increasing appreciation for the importance of inflammation as a pathophysiologic entity that contributes to functional gastrointestinal disorders including functional dyspepsia (FD). Importantly, inflammation may serve as a mediator between psychologic and physiologic functions. This manuscript reviews the literature implicating two inflammatory cell types, mast cells and eosinophils, in the generation of dyspeptic symptoms and explores their potential as targets for the treatment of FD. There are a number of inciting events which may initiate an inflammatory response, and the subsequent recruitment and activation of mast cells and eosinophils. These include internal triggers such as stress and anxiety, as well as external triggers such as microbes and allergens. Previous studies suggest that there may be efficacy in utilizing medications directed at mast cells and eosinophils. Evidence exists to suggest that combining "anti-inflammatory" medications with other treatments targeting stress can improve the rate of symptom resolution in pediatric FD.