Atrial fibrillation (AF) is the recognized risk factor for hemorrhagic transformation (HT) in thrombolysis patients with acute ischemic stroke (AIS). But the impact of AF on prognosis is still controversial. In our study, we aimed to assess the relationship between AF and HT and prognosis.We assessed 184 patients diagnosed with AIS and received thrombolysis from January 2016 to October 2017. Based on the imaging results during hospitalization, the patients were divided into HT and non-HT groups in which the HT was containing 40 patients. According to the modified Rankin Scale (mRS), we divided the patients into favorable prognosis (mRS score of 0-2) and the poor (mRS score >2) after 3 and 6 months of follow-up. Our analysis included demographics, onset to treatment time, initial blood pressure, baseline National Institutes of Health Stroke Scale (NIHSS) score, HT, anticoagulants, AF, smoking, and other past history.At baseline, there was a significant difference (p < 0.05) between the HT and non-HT groups in the level of age, hyperlipidemia, AF, NIHSS, and the application of anticoagulants. After 3 and 6 months of follow-up, we found that only NIHSS (OR3 month 1.421, 95% CI 1.280-1.578, p < 0.001, and OR6 month 1.326, 95% CI 1.217-1.445, p < 0.001) was associated with prognosis instead of AF, HT, and anticoagulants. Meanwhile, patients with AF tended to be older, higher NIHSS score and less hyperlipidemia (p < 0.05).The present study indicated that there is no significant correlation between AF and prognosis, although there is some indeed related with HT. That was, the prognosis with AF had a similar response trend compared with the non-AF.