Controversies exist regarding the treatment of acute massive pulmonary embolism (PE) with anticoagulation alone or with thrombolytic therapy. Paradoxical embolism in the presence of a patent foramen ovale (PFO) is a rare but well-known entity and should always be looked for in case of a PE associated with systemic thromboembolism. We report a case of acute sub-massive PE treated with thrombolytic therapy in an elderly gentleman who had a paradoxical embolism and ischemic stroke as a result of a clot traversing through a PFO. We discussed diagnostic modalities, treatment of choice, and associated controversies in management.