Background <p>Impending paradoxical embolism (IPDE) is a rare condition characterized by the presence of a thrombus in a patent foramen ovale. We were able to image a thrombus lodged in a patent foramen ovale and remove the thrombus before it could result in arterial embolism.</p> Case presentation <p>A 24-year-old woman was admitted to our hospital with chest pain and dyspnea. Pulmonary embolism was diagnosed via computed tomography. Additionally, transesophageal echocardiography revealed a thrombus lodged in a patent foramen ovale and fluttering in both atria, leading to a diagnosis of IPDE. Rather than incurring the risk associated with embolization by thrombolytic treatment, we elected to remove the incarcerated thrombus and close the patent foramen ovale under cardiopulmonary bypass.</p> Conclusions <p>We successfully treated a case of IPDE by removing the thrombus under cardiopulmonary bypass, before arterial thrombosis could occur.</p>