Background: Atrial fibrillation (AF) is the most common cardiac arrhythmia with a prevalence of 15% of patients over 80 years. Coronary artery disease co-exists in 20–30% of patients with atrial fibrillation. The need for triple anticoagulation therapy makes the management of these patients challenging following PCI. Methods: Nationwide inpatient sample which is a set of longitudinal hospital inpatient databases was used to evaluate the outcome of patients with AF who underwent PCI. All patients undergoing PCI between 2002 and 2011 were included in the study. Specific ICD-9-CM codes were used to identify the study patients and their outcomes. Results: There were 3,226,405 PCIs during the time period of the study of which 472,609 (14.6%) patients had AF. AF patients were older and predominantly male (60%). The number of PCIs had a declining trend from 2002 to 2011. Age adjusted inpatient mortality was significantly higher in PCI AF group compared to the PCI non-AF group (100.82 ± 9.03 vs 54.07 ± 8.96 per 100,000; P < 0.01). Post PCI predictors of mortality were AF (OR 1.56, CI 1.53–1.59), CKD (OR 1.41, CI 1.37–1.46), PAD (OR 1.20, CI 1.15–1.24), acute myocardial infarction (OR 2.42 CI 2.37–2.46 and cardiogenic shock (OR 13.92 CI 13.60–14.24) P < 0.001. Conclusion: AF is common in patients undergoing PCI and those AF patients have a higher age-adjusted all cause inpatient mortality. There is a decline in total number of PCIs over time in US. Atrial fibrillation, chronic kidney disease, peripheral artery disease, MI and cardiogenic shock were associated with increased mortality following PCI.