Patients with inflammatory bowel disease (IBD) have been reported to have an increased risk of thromboembolism. Cerebral venous thrombosis (CVT) is a rare but serious extraintestinal manifestation of IBD. Due to its highly variable manifestation and low incidence, CVT is not usually readily recognized by physicians. Herein, we report a case of a 35-year-old male presenting with CVT associated with ulcerative colitis (UC). The patient was admitted with chief complaints of bloody diarrhea that had started 3 days prior. Sigmoidoscopy showed hyperemic and edematous mucosa, friability, and shallow ulcers from the sigmoid colon to the rectum suggestive of IBD. Three days later, the patient started complaining of a headache, and gradually developed a decreased level of consciousness. Magnetic resonance imaging of the brain revealed CVT with hemorrhagic infarctions. An angiogram was obtained to evaluate the extent of CVT, and anticoagulation therapy was initiated with intravenous heparin. During hospitalization, he was diagnosed with UC and treated with 5-aminosalicylic acid. After discharge, the patient was recovered without neurological deficit, and remission of UC was also obtained. The presence of headache or acute worsening of neurological status in a patient with IBD should alert the health professionals about the possibility of CVT.