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Background Behçet’s syndrome is a type of systemic chronic vasculitis of unknown etiology, frequently characterized by recurrent oral and genital ulcers and uveitis. It is less commonly characterized by arthritis and skin, vascular, and gastrointestinal involvements. Behçet’s syndrome affects various sizes of vessels by perivascular infiltration and vasculitis. Unlike other classic types of vasculitis, Behçet’s syndrome patients can present with both arterial and venous involvement. Although vascular Behçet’s syndrome is found in only around 15% of Behçet’s syndrome patients, it is the major cause of morbidity and mortality among them. Furthermore, although deep venous thrombosis has high incidence in Behçet’s syndrome patients, pulmonary artery thrombosis is an uncommon complication. Combining the findings of this and previous case reports of pulmonary artery thrombosis in Behçet’s syndrome patients, we sought to determine the best treatment options for pulmonary artery thrombosis in Behçet’s syndrome patients. Case presentation We present the case of a 22-year-old Arabian male who was admitted to an emergency department with acute chest pain, dyspnea, and hemoptysis for 2 weeks. He gave a long history of recurrent oral and genital ulcers for the last 4 months but without seeking medical advice. Spiral computed tomography showed arterial filling defects with a pulmonary nodule for which the presence of a pulmonary artery aneurysm ruled out. The lung perfusion scan showed multiple pulmonary perfusion defects. After excluding common infectious diseases such as tuberculosis and brucellosis, a diagnosis of Behçet’s syndrome with pulmonary artery thrombosis was made. Steroids with enoxaparin were initiated. The patient was discharged later on prednisolone (tapering dose) with adalimumab and apixaban. He was on regular follow-up for the next 9 months. Conclusions Vascular involvement in Behçet’s syndrome is a major contributor to morbidity and mortality of Behçet’s syndrome patients. Consequently, early detection of vascular involvement has a major impact on the prognosis of patients with Behçet’s syndrome.