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Background: The most common gastrointestinal disorders are functional gastrointestinal disorders (FGID) of which functional indigestion is one of the most common types and causes the deterioration of ‎health and reduction of quality of life (QOL). This study was conducted with the aim to determine the effectiveness of emotion regulation training on metacognitive beliefs and pain perception in patients with functional indigestion. Methods: The present study was a quasi-experimental research with pretest-posttest design and a control group. The statistical population consisted of all patients with functional indigestion in Tehran, Iran, in 2020. The sample consisted of 30 patients who were selected through the convenience sampling method and randomly assigned to an experimental group (emotion regulation training) and a control group (each consisting of 15 people). The research tools included the Metacognitions Questionnaire (Wells & Cartwright-Hatton, 2004) and McGill Pain Questionnaire (Melzack, 1975). Data analysis was performed using analysis of variance in SPSS software. Results: The findings showed that emotion regulation training was effective on metacognitive beliefs (P < 0.001) and pain perception (P < 0.001) in patients with functional indigestion. Conclusion: It can be concluded that emotion regulation training was effective on metacognitive beliefs and pain perception in patients with functional indigestion.