Abstract Background The urgency of the problem of gastroesophageal reflux disease (GERD) in pediatrics is due to the high prevalence of this pathology in children. The problem of GERD in childhood has become especially important, when a direct correlation between the duration of esophagitis and the development of Barrett's esophagus (BE) and, later, esophageal adenocarcinoma has been revealed. Photodynamic therapy (PDT) is used as one of the elements of complex treatment after antireflux surgeries for direct impact on metaplastic mucosa and restoration of normal esophageal lumen. Due to the increased detection of esophageal malignancies in adult patients, we aimed to investigate this method in the treatment of Barrett's esophagus in children. Methods There were 3 patients diagnosed with esophageal mucosal metaplasia in the thoracic surgery department. Intestinal esophageal metaplasia was detected and histologically confirmed in 1 patient, in 2 patients - gastric metaplasia of cardiac type. All patients were female. The average age of the patients was 15 years. Children underwent multiple sessions of balloon dilatation of esophageal stenosis with temporary positive effect. Taking into account persistent restenosis, presence of metaplasia areas we applied PDT. Intravenous injection of photosensitizer (PS) of chlorine series for 30 minutes was carried out 5 hours before the beginning of PDT. For PDT we used a laser unit with a wavelength of 662 nm, power of 1 W with exposure of 25-30 minutes (at the rate of 300 J/cm2), optical power meter, video gastroscope, spectroanalyzer. Results To achieve the result: complete destruction of metaplasia sites and recanalization of the esophageal lumen, 1 patient with intestinal metaplasia needed 3 sessions, 2 patients with gastric metaplasia of cardiac type - 4 sessions of PDT. In children with gastric metaplasia, an "initiation" method was developed and applied at first PDT session to induce inflammation in the esophageal mucosa. During PDT macroscopic changes of mucosa in the metaplasia area were registered: ischemia, edema and hyperemia, hemorrhagic manifestations, "parchment" mucosa. We were also focused on the amount of PS in tissues according to the graphic images of the spectroanalyzer. During control examinations we noted healing of the metaplasia zone with subsequent regeneration of the epithelium, which was confirmed histologically, and preservation of the normal esophageal lumen. Conclusion Thus, there is a possibility of effective use of photodynamic therapy for esophageal mucosal metaplasia in children and adolescents. Taking into account the minimally invasive technique, comparative cheapness of photosensitizers, equipment for generation of laser radiation, registration of photosensitizer concentration in tissues, it is possible to create the basis for conducting studies in the treatment of this pathology in children. The method of photodynamic therapy in Barrett's esophagus demonstrates high efficiency in its eradication. Increasing the number of observations will allow to make more meaningful conclusions in the future. Eradication of Barrett's esophagus in children meets the requirements of cancer vigilance.