Relationships between gut microbiota and various disease pathogeneses have been investigated, but those between the pathogeneses of mental illnesses, including schizophrenia, and gut microbiota have only recently attracted attention. We observed a change in the gut microbiota of a patient with schizophrenia after administering electroconvulsive therapy (ECT). A 59-year-old woman was diagnosed with schizophrenia at 17 years of age and has been taking antipsychotic drugs since the diagnosis. Clostridium, which occupied 86.5% of her bacterial flora, decreased to 72.5% after 14 ECT sessions, while Lactobacillus increased from 1.2% to 5.5%, and Bacteroides increased from 9.1% to 31.5%. Previous studies have shown that Clostridium spp. are increased in patients with schizophrenia compared with those in healthy individuals and that Clostridium is reduced after pharmacological treatment. Our report is the first report on the gut microbiota of a patient with schizophrenia receiving ECT. Our results indicate that studies focusing on Clostridium to clarify the pathogenesis of schizophrenia as well as potential therapeutic mechanisms may be beneficial. However, further studies are needed.