Summary Background While prior studies have demonstrated that chronic obstructive pulmonary disease (COPD) is associated with gastroesophageal reflux disease (GERD), and that GERD is associated with acute exacerbations of COPD (AECOPD), no study to date has been able to establish temporality in this relationship. The purpose of this cohort study was to explore the impact of a new diagnosis of GERD on the risk of subsequent AECOPD. Methods We used a retrospective population-based cohort design to analyse the data of 1976 COPD subjects with GERD as an exposure cohort and 3936 COPD subjects without GERD as a comparison group. We individually tracked each subject in this study for 12 months and identified those subjects who experienced an episode of AECOPD. Hazard ratios (HR) were calculated using Cox proportional hazards regression analysis. Results The incidence of AECOPD was 4.08 and 2.79 per 100 person-year in individuals with and without GERD, respectively (p = 0.012). Following adjustment for sex, age, ischaemic heart disease, heart failure, atrial fibrillation, hypertension, osteoporosis, anxiety, diabetes mellitus, angina, stroke, anaemia, dementia, occupational category, monthly insurance premium, number of OPD visits and COPD severity. The stepwise Cox regression analysis revealed that GERD was independently associated with an increased risk of AECOPD (HR = 1.48, 95% CI = 1.10-1.99). Conclusion This study demonstrated that GERD is an independent risk factor for AECOPD. Caution should be exercised when assessing GERD symptoms in patients with COPD.