BACKGROUND AND AIM: Functional gastrointestinal disorders are a group of stress-sensitive gut-brain disorders. The COVID-19 outbreak has caused immense stress and anxiety among the general public. Strict measures to counter COVID-19 emergency, including physical distancing, have also taken a toll on physical and mental health. We investigated the impact of the COVID-19 pandemic on the gastrointestinal and psychological symptoms of functional dyspepsia (FD) and irritable bowel syndrome (IBS). METHODS: An online survey was conducted in Japan for a group of randomly assigned panelists from May 26 to 27, 2020. Each respondent answered a questionnaire on stress, physical distancing, and worries about COVID-19. Gastrointestinal symptoms were assessed to diagnose FD and IBS (Rome III), and psychological symptoms were assessed using the Hospital Anxiety and Depression Scale. RESULTS: A total of 5157 subjects were finally enrolled, with FD in 8.5%, IBS in 16.6%, and FD-IBS overlap in 4.0%. For both gastrointestinal and psychological symptoms, respondents with FD-IBS overlap showed the worst scores, followed by IBS-alone, then FD-alone respondents. During the COVID-19 pandemic, 11.9% of respondents reported deterioration and 2.8% reported improvement of gastrointestinal symptoms. FD-IBS overlap, psychological disease comorbidity, and stress at work/school were significantly associated with symptom deterioration. Younger age, commuting by public transport, and work/study from home were associated with symptom improvement. CONCLUSIONS: The COVID-19 pandemic negatively affected FD/IBS subjects, with respondents showing FD-IBS overlap syndrome as the most important independent factor associated with deterioration in gastrointestinal symptoms. Physicians need to take extra care of FD/IBS patients in the post-COVID period.