Background It has been widely reported that anticoagulants (ACs) are underused for primary and secondary prevention of ischemic stroke in patients with atrial fibrillation (AFib). Furthermore, precise evidence-based guidelines about the best timing for AC initiation after acute stroke are currently lacking. Methods and Results In this retrospective, observational study, we analyzed prescription trends in AFib patients with acute ischemic stroke who were hospitalized in four neurologic stroke units of our region (Lombardia, Italy). In-hospital antithrombotic prescription was performed in highly heterogeneous patterns. A prestroke treatment with AC was the leading factor enhancing AC prescription during hospitalization. The other factors promoting AC were male gender, younger age, lower prestroke disability and stroke severity, and smaller stroke volumes. AFib subtype influenced AC prescription only in AC-naïve patients. Interestingly, Congestive heart failure, Hypertension, Age higher than 75 years, Diabetes, previous Stroke or TIA or thromboembolism, Vascular disease, Age 64–75 years, female Sex (CHA2 DS2 -VASc) and Hypertension, Abnormal renal and liver function, Stroke, Bleeding, Labile INRs, Elderly, Drugs and alcohol (HAS-BLED) scores were not associated with AC prescription. However, patients who were treated with AC, including early treatment (<48 hours), showed a low rate of bleeding. Conclusions Our findings potentially suggest that, although apparently neglecting the common risk stratification tools, our neurologists were able to select the more suitable candidates for prompt AC treatment. Further studies are needed to develop new scoring systems to aid ischemic and hemorrhagic risk estimation in the secondary prevention of stroke.