Exercise intolerance among the clinical symptoms in patients with atrial fibrillation (AF) has usually been masked by their adjusted life style. We sought to assess the role of CHA2DS2-VASc score to predict exercise intolerance in asymptomatic AF patients, and further examine whether the relationship differs by age and gender. Among the 6,275 participants of the prospective Korean registry of the Comparison study of Drugs for symptom control and complication prevention of Atrial Fibrillation (CODE-AF), 1,080 AF patients who underwent exercise treadmill testing were studied. Exercise intolerance was defined as a peak exercise capacity of 7 metabolic equivalents (METs) or less, and the patients were divided into two groups for the analysis: ≤7 METs (n = 131) and >7 METs (n = 949). Patients with exercise intolerance had a significantly higher CHA2DS2-VASc score than those without (3.1 ± 1.3 vs. 2.0 ± 1.5, p < 0.0001). In the multivariate analysis, a higher CHA2DS2-VASc score (OR 1.54, 95% CI 1.31–1.81, p < 0.0001), corrected QT interval (OR 1.01, 95% CI 1.00–1.02, p = 0.026), and increased left atrial volume index (OR 1.02, 95% CI 1.01–1.03, p = 0.001) were found to be independent predictors of exercise intolerance. The impact of the CHA2DS2-VASc score on exercise intolerance was significant only in male patients aged <65 years (OR 3.30, 95% CI 1.76–6.19, p < 0.0001). The CHA2DS2-VASc score may be a feasible risk assessment tool to predict exercise intolerance, especially in young and middle-aged male patients with asymptomatic AF.