Background and purpose: A higher CHADS2 score or CHA2DS2-VASc score is associated with an increased risk of ischaemic stroke in patients with non-valvular atrial fibrillation (NVAF). However, there are no data regarding early neurological outcomes after stroke according to the risk levels. Methods: In this study, a total of 649 stroke patients with NVAF were enrolled and categorized into three groups: low-risk (CHADS(2) score of 0-1), moderate-risk (CHADS(2) score 2-3), or high-risk group (CHADS(2) score >= 4). CHA(2)DS(2)-VASc score was divided into four groups including 0-1, 2-3, 4-5, and 6. We investigated whether there were differences in initial stroke severity, early neurological outcome, and infarct size according to CHADS(2) score or CHA2DS2-VASc score in stroke patients with NVAF. Results: The initial National Institutes of Health Stroke Scale (NIHSS) score was highest in high-risk group [9.5, interquartile range (IQR) 4-18], followed by moderate-risk (8, IQR 2-17) and low-risk group (6, IQR 2-15) (P = 0.012). Likewise, initial stroke severity increased in a positive fashion with increasing the CHA(2)DS(2)-VASc score. During hospitalization, those in the high-risk group or higher CHA(2)DS(2)-VASc score had less improvement in their NIHSS score. Furthermore, early neurological deterioration (END) developed more frequently as CHADS(2) score or CHA(2)DS(2)-VASc score increased. Multivariate analysis showed being in the high-risk group was independently associated with END (OR 2.129, 95% CI 1.013-4.477). Conclusions: Our data indicate that patients with NVAF and higher CHADS(2) score or CHA(2)DS(2)-VASc score are more likely to develop severe stroke and a worse clinical course is expected in these patients after stroke presentation.