Abstract Background Patients with atrial fibrillation (AF) who undergo percutaneous coronary intervention (PCI) are recommended to receive dual antithrombotic therapy including an antiplatelet agent and direct anticoagulants (DOAC). We compared the effectiveness between aspirin and clopidodgrel for a combination therapy with DOAC in this population. Methods We analyzed patient data from the Korea National Health Insurance Service. A total of 9,157 patients with AF who received dual antithrombotic therapy after PCI were included. Patients were classified into the aspirin group and clopidogrel group, and 1:1 propensity score matching (PSM) was performed. The primary ischemic endpoint was a composite of cardiovascular death, myocardial infarction, stroke, or systemic thromboembolism. A major bleeding event was defined as a bleeding event requiring hospitalization. Results After PSM, there were each 2,882 patients each in the aspirin and clopidogrel group. The incidence of the primary ischemic endpoint was similar in the two groups (22.8% vs. 21.8%, in the aspirin and clopidogrel group, hazard ratio [HR] for clopidogrel group: 0.909, 95% confidence interval [CI] 0.815 – 1.014). The incidence of each component of ischemic endpoint did not differ significantly between the two groups. All-cause mortality was increased in the clopidogrel group (HR 1.301, 95% CI 1.000 – 1.692). There was no significant difference in major bleeding events (HR 0.942, 95% CI 0.789 – 1.126). Conclusions For a dual antithrombotic therapy in patients with AF who had undergone PCI, aspirin and clopidogrel did not differ in terms of ischemic outcomes, but the use of aspirin was associated with slightly lower all-cause mortality.