In this study, we aimed to examine the association between atrial fibrillation and mortality after ischemic stroke and evaluate the use of anticoagulation therapy for atrial fibrillation before stroke onset in patients who experienced stroke. In this retrospective observational study, we used a combined database of medical and long-term care insurance claims data from one prefecture in Japan. The data of 25,352 patients aged ≥65 years who were hospitalized in acute care hospitals with a diagnosis of ischemic stroke between April 2012 and March 2015 were extracted. Cox proportional hazard modeling, with adjustment for age, sex, comorbidities, and long-term care dependency level (based on the activities of daily living), was performed to evaluate the relationship between mortality and atrial fibrillation. The prevalence of atrial fibrillation was 21.8% in the study population. A significant association was noted between mortality and atrial fibrillation (adjusted hazard ratio: 1.28, 95% confidence interval: 1.16–1.41, p < 0.001). Anticoagulant drugs were used in 32.2% of the patients with atrial fibrillation. These results indicate that atrial fibrillation is associated with mortality after stroke; however, the use of anticoagulation therapy for atrial fibrillation is unsatisfactory. Efforts to improve the use of atrial fibrillation therapy are required in Japan.