Abstract Aims Patent foramen ovale (PFO) is associated with a variety of clinical events; however, its association with major adverse cardiovascular events (MACEs) in patients with coronary artery disease (CAD) remains unclear. The objective of our study was to compare the prognosis between patients with and without PFO and to investigate the association between PFO and MACEs in patients with CAD. Methods and Results This study retrospectively included 2667 patients who underwent coronary computed tomography angiography (CCTA) for the evaluation of suspected CAD. MACEs were defined as cardiac death, non-fatal myocardial infarction, and ischemic stroke. The primary endpoint was a composite of cardiac death and non-fatal myocardial infarction. The secondary endpoint was defined as ischemic stroke. After a median follow-up of 86 months [interquartile range: 74–99 months], 288 patients experienced MACEs, among whom 203 patients had the primary endpoint and 85 patients had the secondary endpoint. Compared with patients without PFO, patients with PFO had a higher cumulative incidence of MACEs (P<0.001), as well as higher cumulative incidence rates for both the primary endpoint (P<0.001) and secondary endpoint (P<0.001). PFO was significantly associated with MACEs in patients with CAD (HR=3.82, P<0.001). In multivariate analysis, PFO remained an independent predictor of MACE in patients with CAD (HR=2.98, P<0.001), with consistent results observed in the analyses of both the primary endpoint and secondary endpoint (All P<0.001). Conclusion PFO is associated with adverse prognosis in patients with CAD, and patients with PFO have a higher risk of MACEs.