Background: The population of adults with congenital heart diseases (ACHDs) is expanding, and atrial fibrillation (AF) emerges as a crucial risk factor for ischemic stroke. However, the evidence regarding the impact of AF on the incidence of ischemic stroke in ACHDs remains limited. In this study, we aimed to investigate the prevalence and effect of AF among ACHDs and assess the suitability of the traditional CHA₂DS₂-VASc score in this specific population. Methods: Data of ACHDs from 2000 to 2010 were retrospectively collected from the Taiwan National Health Insurance Research Database. We divided ACHDs into those with and without AF, and ischemic stroke incidence was studied among ACHD subtypes and those who received anticoagulant therapy with warfarin or not according to CHA₂DS₂-VASc score. Results: 36,530 ACHDs were retrieved from the database. ACHDs had a 4.7–15.3 times higher AF risk than did the general population, which varied based on the age group. ACHDs with AF had 1.45 times higher ischemic stroke risk than those without AF (p = 0.009). Ischemic stroke incidence among ACHDs with AF aged 50 years was 1.46 times higher than those without AF (p = 0.207). Ischemic stroke incidence was over 1.47% even in those with a low CHA₂DS₂-VASc score (0–1) with or without anticoagulant therapy. Conclusions: During the 12-year follow-up, ACHDs with AF were found to have an increased risk of ischemic stroke. The ischemic stroke incidence was high, even in those with a low CHA₂DS₂-VASc score (0–1).