Orthodontic patients with malocclusion have significantly lower masticatory and gastrointestinal digestive function than persons with normal occlusion. Although several studies have suggested that masticatory function is improved after orthodontic treatment, the relationship between such improvement and change in gastrointestinal symptoms has not been quantitatively evaluated. In this study, we aimed to investigate the change in masticatory function and the gastric emptying rate in patients with malocclusion, before and after orthodontic treatment. Seven women with malocclusion, before (pretreatment group) and after orthodontic treatment (posttreatment group), and 7 healthy dentate female volunteers (control group) underwent a 13C-acetate breath test (13CO2) with a liquid meal and the color changeable gum test, along with completing the frequency scale for symptoms of gastroesophageal reflux and a questionnaire on food intake. Between-group differences were evaluated. The pretreatment group had significantly longer maximum 13CO2 exhalation time and lower masticatory function, quantified using a higher red-color value on the gum test and the questionnaire on food intake, than did the posttreatment and control groups. No significant differences were identified between the posttreatment and the control groups. We provide evidence of improvement of masticatory function after orthodontic treatment, which was associated with a faster rate of gastric emptying.