Introduction Erectile dysfunction (ED) has been regarded a marker of cardiovascular diseases. Nevertheless, the association between ED and incident atrial fibrillation (AF) remains unknown. Aim To determine the association between ED and incident AF. Methods This population-based cohort study was conducted using the National Health Insurance Research Database in Taiwan. In total, 6,273 of patients with ED without a prior diagnosis of AF were enrolled from January 1, 2001 through December 31, 2009, and a propensity-score matching method was used to identify 3,516 patients in the ED and control groups. Main Outcome Measures Newly incident AF at follow-up was recorded as the end point. Results The mean age of the study population was 40.0 ± 17.1 years, and the follow-up period was 8.0 ± 0.5 years. Compared with the control group, patients with ED were older and had more of the following comorbidities: D’Hoore Charlson Comorbidity Index, hypertension, congestive heart failure, diabetes mellitus, dyslipidemia, chronic kidney disease, coronary artery disease, stroke, chronic lung disease, major depression disorder, obstructive sleep apnea, and hyperthyroidism. After adjusting for confounders, the ED group was not associated with more incident AF compared with the control group (hazard ratio = 1.031, 95% confidence interval = 0.674–1.578, P =.888). In these patients, ED of an organic origin was associated with a trend of having AF more often compared with ED of a psychosexual type (P =.272 by log-rank test). Conclusion Although ED is known as a predictor of atherosclerotic cardiovascular diseases, it is not independently associated with incident AF in men.