Purpose: To study factors associated with poor outcomes in acute ischemic stroke patients with atrial fibrillation (AF) by using a national database. Materials and Methods: This study was a retrospective analytical study by retrieving data from the Thailand national database system for universal coverage (UC) health insurance system. All adult patients aged over 18 years who were admitted with acute ischemic stroke during the fiscal years 2004–2012 by the appropriate ICD codes were searched. Eligible patients with AF were categorized as alive or dead during hospital stay. The mortality rate and factors associated with in-hospital mortality were studied. Results: There were 522,699 patients diagnosed as acute stroke; 277,291 patients (53.1%) had acute ischemic stroke. Of those with ischemic stroke, 25,319 patients (9.1%) had AF. The mortality rates of acute ischemic stroke with AF were 14.1% and without AF were 6.2%, (p < 0.001). Significant factors associated with mortality in acute stroke patients with AF by multivariate logistic regression were female gender (adjusted odds ratio; AOR 1.28), co-morbid diseases such as diabetes (AOR 1.28), hypertension (AOR 1.26), rt-PA treatment (AOR 0.55), and stroke complications, such as pneumonia (AOR 2.60), septicemia (AOR 6.50), or gastrointestinal bleeding (AOR 2.16). Conclusions: At the national level, AF caused a higher mortality rate in acute ischemic stroke than in non-AF patients. Gender, co-morbid diseases, rt-PA treatment, and stroke complications were associated with mortality in acute ischemic stroke with AF.