Upper extremity deep vein thrombosis (UEDVT) is a life threatening rare condition. Among the patients with UEDVT, internal jugular vein is accepted as uncommon thrombosis. Since internal jugular vein thrombosis (IJVT) is mostly underdiagnosed, a great attention is needed to diagnose the disease. A 75-year-old woman with history of dyspnea on exertion (DOE), weight loss and anorexia with the stable vital sign and right-sided cervical adenopathy with suspected thyroid nodule was admitted. One day after admission, sudden dyspnea was occurring with unstable vital sign and hypotension. Chest X-ray showed a bilateral pleural effusion. Pleural tap was exudative, CT scan showed bilateral pulmonary emboli. CT scan of the neck showed right-sided cervical adenopathy, heterogeneous thyroid and internal jugular vein thrombosis concomitant with superior thyroid vein thrombosis. The patient was treated with thrombolytic agent and enoxaparin followed by warfarin. Thyroid FNA revealed papillary thyroid carcinoma that followed by total thyroidectomy, histopathological examination verified papillary thyroid carcinoma. Although lower extremity DVT is the main cause of pulmonary emboli, but IJVT may be proceed by pulmonary embolism. Due to fatal outcome of pulmonary emboli in IJVT, color duplex sonography, is recommended in documented tumors or suspected history of malignancy.