Functional dyspepsia is very common in children of all ages and has a significant impact on the patient's family and quality of life. Since the revision of the Rome IV criteria with the introduction of two subtypes, the prevalence of functional dyspepsia has increased, but currently no guidelines for the treatment are available. The aim of this study was to characterize patients, who have been diagnosed with functional dyspepsia and analyze the outcome of different treatments they received. This is a retrospective study of pediatric patients, diagnosed with functional dyspepsia between March 2017 and September 2020. All patients aged between 0 and18 years, who complained about gastric symptoms, have had a normal full blood count, a normal thyroid function, a negative coeliac screening, and most importantly normal macro- and microscopic findings on esophago-gastro-duodenoscopy were included in the study. Patient's data were extracted from the medical record and three months after the performance of the endoscopy, parents were interviewed about the effect of the treatment. A total of 154 patients (66.2% female, 33.8% male) between the age of 4 and 18 years were included. In 113 (73.4%) the leading symptom was epigastric pain, followed by nausea (22; 14.3%) and a fifth of the patients (females: 18.6%; males: 21.2%) self-reported a current stressor in clinic. After receiving the diagnosis of a functional nature, families chose following treatments: 50 STW5 (32.3%, overall, 10.4% added dietary changes, alternative treatment, and psychology support), psychological support (22.7%), alternative treatments (e.g., hypnotherapy, meditation; 19.5%), dietary changes (12.9%), lifestyle changes (9.7%), no treatment (11%) and in 10.4% no treatment was needed as symptoms resolved after endoscopy had been performed. Only lifestyle changes (p = 0.03) in females, dietary changes (p = 0.035 for girls, p = 0.06 for boys) and STW5 in males (p = 0.043) showed a statistically relevant correlation regarding duration of symptoms. There was no correlation between location of symptoms and effectiveness of treatment. It is recommended to treat patients from both subgroups of functional dyspepsia differently, in accordance with the currently available explanatory models of underlying pathophysiological processes. In this cohort of patients this could not be verified. As all patients did benefit from any treatment, it is likely that the treatment itself was not accountable for the relief of symptoms, but that most patients benefit from education on the diagnosis, reassurance and a recommendation of a healthy lifestyle. Some patients might benefit from medications, small changes in the diet, psychological support or alternative treatment, but success depends on individual, unpredictable factor.