An adolescent with a recent diagnostic of Behçet's Disease (BD) was admitted with fever and intracardiac lesions detected on a routine transthoracic echocardiography, suggestive of endocarditis. Due to the absence of improvement after several rounds of antibiotics the patient was submitted to contrast-enhanced cardiac MRI that showed signs of intracardiac thrombosis, superior vena cava syndrome and pulmonary thromboembolism. The patient underwent surgery to excise the lesions and has been treated with cyclophosphamide and high dose prednisolone achieving complete remission. Intracardiac thrombosis is a rare manifestation of BD, and is associated with a poor prognosis. These patients usually require a combination of anticoagulation and immunosuppression to achieve remission.