Background: Several cardiovascular diseases exhibit seasonal variations, but data about cold temperature and risk of ischemic stroke in patients with atrial fibrillation (AF) are limited. Objective: The purpose of this study was to investigate the risk of ischemic stroke in different seasons, testing the hypothesis that the cold weather season would increase the risk of stroke in AF. Methods: This study used the National Health Insurance Research Database in Taiwan. From 2000 to 2012, a total of 289,559 AF patients were enrolled, and 34,991 experienced ischemic stroke after mean follow-up of 3 years. The relationship between risk of ischemic stroke and temperatures was analyzed. Results: The highest incidence of ischemic stroke was observed in winter, which was the coldest season, with an incidence rate of 0.33 per 100 person-months. Compared with the summer period, the risk of ischemic stroke increased by 10% in spring (incidence rate ratio [IRR] 1.10; 95% confidence interval [CI] 1.07–1.13) and by 19% in winter (IRR 1.19; 95% CI 1.15–1.22) but did not differ significantly between summer and autumn (IRR 1.00; 95% CI 0.97–1.03). Compared with the days with an average temperature of 30°C, the risk of ischemic stroke for days with an average temperature <20°C significantly increased. Lower 7-, 10-, or 14-day average temperatures were significantly associated with an increased risk of ischemic stroke in the case-crossover analysis. Conclusion: In this nationwide study, a seasonal variation of incidence of ischemic stroke in AF patients was observed, with an increased risk of stroke on days with an average temperature <20°C. AF-related stroke may be influenced by environmental interactions.