BACKGROUND AND PURPOSE The stroke severity on admission and clinical outcomes were compared between ischaemic stroke patients with non-valvular atrial fibrillation (NVAF) of the persistent (PeAF) and paroxysmal (PAF) types. METHODS The study comprised 9293 patients with cardioembolic stroke and NVAF who were registered in the Japanese stroke databank: 6522 had PeAF (70.2%) and 2771 had PAF (29.8%). Stroke severity on admission and the clinical outcomes on discharge were retrospectively compared between these patient groups. RESULTS The National Institutes of Health Stroke Scale score on admission (median, interquartile range) was 10 (3-20) for PeAF patients and 7 (2-17) for PAF patients, indicating that stroke severity on admission was significantly worse in PeAF patients than PAF patients (P < 0.001). Good outcomes (modified Rankin scale score ≤2) were achieved by 45% PeAF patients and 53% PAF patients. Thus, PeAF patients had significantly poorer clinical outcomes than PAF patients (P < 0.001). In-hospital mortality was significantly higher amongst PeAF patients (11%) than PAF patients (8%) (P < 0.001). Multivariate analysis of factors contributing to clinical outcomes showed that PeAF was a contributing factor for in-hospital mortality (odds ratio 1.261; 95% confidence interval 1.011-1.652; P = 0.045). CONCLUSIONS Amongst cardioembolic stroke patients with NVAF, those with PeAF have significantly higher stroke severity on admission than those with PAF, and PeAF is a factor contributing to in-hospital mortality. Thus, our study suggests that the type of atrial fibrillation affects stroke severity and clinical outcomes following cerebral infarction.