Right heart thrombi can be seen in a minority of patients with acute pulmonary embolism and are associated with an increased mortality risk. The optimal treatment option comprises thrombolysis or surgical thrombectomy either with catheter- based interventions or with open surgery. Open right atrial thrombectomy is usually performed under cardiopulmonary bypass due to the need for concomitant pulmonary embolectomy. Nevertheless, cardiopulmonary bypass has major drawbacks such as the risk of stroke, coagulopathy, and myocardial and respiratory dysfunction, particularly in high-risk patients. Herein, we report a case of successful off-pump surgical thrombectomy performed for the right atrial clot-in-transit following failure of the catheter-based intervention.