When more patients with congenital heart disease reach adult age, increased incidence of long-term complications, including ischemic stroke, are expected. The aim of this study was to analyze cumulative incidence of ischemic stroke, associated factors, and case fatality in adult congenital heart disease. The study is based on Swedish national registers on congenital heart disease and stroke. Patients with congenital heart disease were followed between 2001 and 2018 for first-ever ischemic stroke events (ischemic stroke due to patent foramen ovale excluded). Factors possibly associated with ischemic stroke were analyzed using Cox regression models. Out of 8914 adult patients with congenital heart disease, 108 suffered ischemic stroke over a mean period of 7.6±4.7 years. The mean age at ischemic stroke was 53.8 years, and the cumulative incidence was 0.15% at 1 year, 0.5% at 5 years, and 1.5% at 10 years. In multivariable analysis, age (hazard ratio [HR], 1.04 [95% CI, 1.03-1.06]), diabetes (HR, 2.9 [95% CI, 1.3-6.4]), ejection fraction <50% (HR, 1.9 [95% CI, 1.1-3.4]), atrial septal defect (HR, 3.0 [95% CI, 1.03-8.5]), and aortic valve lesions (HR, 4.8 [95% CI, 1.6-14.1]) were associated with increased risk. Among those with ischemic stroke, approximately half were on antithrombotic treatment (anticoagulants or antiplatelets) before admission. Case fatality was 6.5%. The cumulative incidence of ischemic stroke was 1.5% after 10 years. In adult congenital heart disease, the type of heart lesion, diabetes, ejection fraction <50%, and age were important factors associated with ischemic stroke. Despite a relatively young age, mortality is a significant threat. At time of the ischemic stroke event, approximately half of the patients were on antithrombotic treatment.