A 29-year-old man with ulcerative colitis was admitted to our hospital because of convulsions and a headache. Before admission, oral prednisolone had been administered due to his ulcerative colitis relapse. Computed tomography revealed a low-density area in the right frontal pole suggestive of a venous infarction. Once his headache and convulsions improved after the administration of an antiepileptic drug, he began to complain of right arm numbness and right hemianopsia again. An urgent magnetic resonance imaging angiograph showed extensive thrombosis in the superior sagittal sinus. We finally used the anticoagulant agents, heparin and urokinase, which eased his complaints and prevented the development of bloody stools. He was discharged with no neurological symptoms 25 days after admission. This is a rare case of sinus thrombosis complicated by ulcerative colitis, in which anticoagulant therapy was successful. Magnetic resonance imaging angiography was useful for the diagnosis and for evaluating the therapeutic effect.