Patients with atrial fibrillation (AF) who underwent percutaneous coronary intervention (PCI) are recommended to receive oral anticoagulants (OAC) and concomitant antiplatelet agents followed by OAC monotherapy continued beyond a year after PCI. However, long-term prescription patterns of antithrombotic therapy in real-world clinical practice were not fully investigated. From the National Health Insurance Service database of Korea, we obtained records of patients with AF who underwent PCI between 2009 and 2013. Patients without repeated PCI or death within 2 years following the procedure were included. Prescription records of antithrombotic therapy including anticoagulants and antiplatelet agents were reviewed at 3-month intervals after discharge. We investigated 8,891 patients. At discharge, 76.1% of the patients received dual antiplatelet therapy (DAPT) and only 17.1% received OAC. Although the proportion of patients receiving DAPT gradually decreased, >70% of patients received only antiplatelet agents (DAPT or single antiplatelet therapy) a year after PCI. During the 2-year follow-up, the proportion of patients receiving OAC remained <20%, and only 1.5% of the patients received OAC monotherapy a year after PCI. Female gender, previous myocardial infarction, peripheral vascular disease, and prescription of DAPT at discharge were associated with underprescription of OAC a year after PCI. In conclusion, a significant proportion (76%) of patients with AF who underwent PCI were not prescribed OAC at discharge despite the high risk of stroke contrary to the current guidelines. Most patients continued to receive antiplatelet agents without OAC beyond the 1-year time point after PCI.