Behçet’s disease (BD) is a multisystemic inflammatory disease. Diagnosis is difficult in patients who do not fully meet the diagnostic criteria. A 9-year-old male patient presented with right common and deep femoral vein thrombosis. Low-molecular-weight heparin (LMWH) was administered due to deep venous thrombosis. The patient developed pulmonary embolism on the 9th day of treatment. LMWH was discontinued, and unfractionated heparin (UFH) with tissue plasminogen activator (tPA) combination was given for 5 days. After discontinuation of tPA treatment, UFH was continued. On the 20th day of treatment, the patient developed another thrombosis in the left iliac vein and embolism in the anteromedial-basal segmental branches of the left pulmonary artery. tPA was re-administered. The positron emission tomography/computed tomography (PET/CT) findings supported vascular inflammation in the inferior vena cava and popliteal vein. The patient was diagnosed with incomplete BD due to uveitis and thromboses coexisting with vascular inflammation. PET/CT can be used as a tool to examine for vascular inflammation that would support BD in patients with anticoagulant and thrombolytic therapy-refractory thrombosis.