Objective To assess the influence of atrial fibrillation on post-thrombolytic hemorrhagic transformation and functional prognosis in acute ischemic stroke patients within different time window. Methods 100 patients with acute posterior-circulation ischemic stroke (onset time within 6 h) were included. All patients were divided into≤ 3 h group and 3~6 h group according to the onset time. All patients were also divided into atrial fibrillation group and non-atrial fibrillation group according to whether having atrial fibrillation. All patients were given urokinase intravenous thrombolysis treatment. The curative effect were compared followed up for 3 months. Results There were 44 (44.0%) patients with onset time within 3h, in which 15 patients with atrial fibrillation and 29 patients without atrial fibrillation. There were 56 (56.0%) patients with onset time 3~6 h, in which 20 patients with atrial fibrillation and 36 patients without atrial fibrillation. There were no effects of atrial fibrillation for the recovery of neural function (P > 0.05). The rate of PH bleeding occurred in patients with atrial fibrillation in 3~6 h group within 24 h was higher than that in patients without atrial fibrillation. The difference was statistically significant (P < 0.05). Followed up for 3 months, we found that There were no effects of atrial fibrillation for the mRS score (P > 0.05). Conclusions The presence of atrial fibrillation is not associated with the prognosis in thrombolytic patients. However, it enhanced the risk of parenchymal hematoma if patients were treated within the time window 3~6 h.