BACKGROUND AND AIM This prospective pilot study investigated whether it is possible to predict the therapeutic response in both the early phase (1 week) and sustained phase (4 weeks) before starting proton pump inhibitor (PPI) therapy for functional dyspepsia (FD) or non-erosive reflux disease (NERD). METHODS We administered rabeprazole 10 mg for 4 weeks to NERD/FD patients, who also answered a modified version of the Frequency Scale for Symptoms of gastroesophageal reflux disease (GERD) (FSSG), which added a pain score to the FSSG. Total score (TS), reflux score (RS), dysmotility score (DS), and pain score (PS) were analyzed. Symptom improvement was defined as ≥ 50% improvement in each score. RESULTS We enrolled 83 patients (age [mean ± SD] 50.8 ± 15.8 years, 29 males, 54 females), of whom 62 could be classified into four groups: achieved symptom improvement within 1 week and maintained it for 4 weeks (Early-R, 40.3%); achieved symptom improvement within 1 week but lost it after 4 weeks (Temp-R, 9.7%); did not achieve symptom improvement within 1 week but did after 4 weeks (Late-R, 9.7%); and no improvement (Non-R, 40.3%). Mean TS, RS, DS, and PS in the Non-R group were significantly higher than in the Early-R group (23.9, 10.5, 11.0, and 2.4 vs 14.3, 6.8, 6.4, and 1.2). However, the Temp-R, Late-R, and Non-R groups could not be distinguished by TS, RS, or DS. CONCLUSION The magnitude of the pretreatment modified FSSG score seemed to be associated with the response at 1 week and 4 weeks.