Functional gastrointestinal disorders (FGIDs), including functional dyspepsia (FD), are common chronic disorders even in the younger population. Physical activity is advocated for patients with FGIDs, although the evidence is insufficient. We investigated the association between the intensity of regular exercise and gastric emptying to determine the effect of physical activity on dyspeptic symptoms. Thirty healthy individuals were selected and divided into three groups (low, moderate, and high) using the index of total exercise intensity in a week. Gastric emptying was evaluated by the ¹³C-acetate breath test. Gastroesophageal reflux symptoms, dyspeptic symptoms, stool forms, scores of anxiety and depression, and scores of sleep quality were also compared. Baseline scores of gastroesophageal reflux symptoms, anxiety, depression, and sleep quality were not different among the three groups. Gastric emptying was significantly faster in low-intensity exercise group than the moderate-intensity exercise group. Although the presence of loose stool and alcohol consumption were also associated with the intensity of regular exercise, these variables were not confounders. In conclusion, the intensity of regular exercise was independently associated with gastric emptying in healthy individuals. These baseline data would be useful for consideration of an optimal exercise intervention for the treatment of FD.