Cerebral venous thrombosis (CVT) is the presence of a blood clot in the cerebral vein, which drains blood from the brain. The presentation of symptoms is highly variable and can range from an isolated headache to coma. While CVT is an uncommon condition, it can be triggered by a number of factors such as birth control or excess estrogen use, dehydration, ear infection, head trauma or injury, obesity, cancer or tumors. This report presents a rare case of CVT caused by the sigmoid sinus (SS) manipulation. A 24-year-old female presented with a pulsatile tinnitus in her right ear. After physical examination and imaging study, the patient was diagnosed with the prominent SS and underwent SS wall reshaping surgery. A simple mastoidectomy was performed and the prominent SS was exposed. Remarkably thin cortical bone over SS was noted, and a bony bridge traversing the exposed SS was left. A piece of conchal cartilage was harvested and inserted under the bony bridge, and bone cement was applied. The patient had immediate resolution of tinnitus after surgery, but encountered headache, fever and recurred tinnitus 5 days later. Magnetic resonance venography (MRV) revealed no obstruction or narrowing of the SS, but a suspicious of CVT with the elevation of D-dimer value. It was suspected that CVT caused by SS manipulation increased the intracranial pressure to cause symptoms and fever. After diagnosis, intracranial pressure control and antithrombotic treatment was applied. The symptoms improved with a use of 1 week medication, and now the patient was discharged with oral intake of warfarin. Additional laboratory test suggested the possibility of underlying autoimmune vasculitis previously unrecognized. The patient was sent to the rheumatology department for further evaluation and treatment. CVT is rare, but can become a life-threatening condition if left untreated. When caught early, CVT can be treated noninvasively using medication. Careful suspicion of irregular symptoms, and proper imaging tests such as MRI venogram or CT venogram are helpful to approach to this uncommon condition. The case demonstrates the necessity of clinical suspicion for CVT after SS manipulation.