Functional dyspepsia is a complex of symptoms characterized by upper abdominal discomfort or pain, nausea, vomiting, bloating, early satiety, and anorexia. Standard pharmacological treatment often has low efficacy and might cause side effects associated with the drugs. Patients with functional dyspepsia which is refractory to drug treatments require other therapeutic options. We report a case of a 52-year-old female with medically refractory functional dyspepsia which was successfully treated using Self Controlled Energo-Neuro Adaptive Regulator (SCENAR) therapy. The initial effect of the treatment was documented after 2 sessions and a considerable improvement after 4 sessions. The treatment continued for 2 weeks and included 12 sessions after which all the symptoms were eliminated without any adverse reactions. The conditions of the patient were monitored for 12 months and no recurrent symptoms were observed. This case report suggests that the use of SCENAR therapy provides efficient results for treatment of drug-resistant functional dyspepsia leading to a marked improvement of the conditions of the patient. Additional clinical studies are required to further investigate the effectiveness of this treatment method in other patients.