Background: Proton pump inhibitors (PPIs), the first-choice agents for the treatment of gastroesophageal reflux disease (GERD), cure most GERD patients, but there are still patients in whom symptom improvement is poor despite remission of esophageal mucosal injury. Since the symptoms of such PPI-refractory GERD patients overlap with functional dyspepsia (FD). In Japan, acotiamide was approved as the world's first drug for FD. Acotiamide is known to improve gastrointestinal tract motility by inhibiting acetylcholine esterase, but the therapeutic effect on the overlap between GERD and FD is unknown. A phase II study on acotiamide has been completed in the U.S. Objective: To study the improvement of symptoms when acotiamide was administered in addition to rabeprazole to treat the overlap between GERD and FD. Patients and methods: This study was conducted as a prospective, single-institution, open-label study. Twenty six patients were enrolled, who had a Grade A or higher mucosal injury according to the Los Angeles (LA) classification as judged by esophagogastroduodenoscopy (EGD) and remnant epigastric symptom, but in whom ECG indicated healing of mucosa after oral administration of 10 mg/day rabeprazole for 8 weeks or more. After examination of background factors, 300 mg/day acotiamide was added to 10 mg/day rabeprazole. The symptoms were examined again after 4 weeks to investigate the therapeutic effect. We used an Izumo scale questionnaire, which scores heartburn, epigastralgia, and epigastric fullness from 0 to 15 points each. Results: Twenty six subjects consisting of 11 males and 15 females were evaluated. Before and after adding acotiamide, heartburn scores were 4.2 and 3.0, respectively, demonstrating a significant decrease (improvement rate, 29%; p=0.044); epigastralgia scores were 3.8 and 3.1, respectively, indicating no significant difference (improvement rate, 18%; p=0.089); epigastric fullness scores were 7.0 and 3.8, respectively, demonstrating a significant decrease (improvement rate, 46%;p=0.0001); total scores of these three epigastric symptoms were 14.9 and 10.0, respectively, demonstrating a significant decrease (p=0.0002). Score decreased by 50% or more in 31% of subjects. Conclusions: Even if PPI administration improves mucosal injury, it is often difficult in clinical practice to treat the overlap between GERD and FD, with which epigastric symptom improvement with PPI treatment is poor. This study suggests that adding acotiamide to PPI is potentially effective in improving the symptoms in treating such patients.