Patients with inflammatory bowel disease (IBD) have an elevated risk of venous thromboembolism compared with the general population. The most common sites of venous thromboembolism in IBD patients are the deep veins of the legs, the pulmonary system, and portal and mesenteric veins. However, cerebral venous thrombosis is rarely associated with IBD. This report describes a case of cerebral venous thrombosis in a patient with Crohn's disease. A 17-year-old girl, diagnosed 4 years earlier with Crohn's disease, presented with headache and vomiting. Magnetic resonance imaging of the brain with venography showed venous thrombosis in the cortical veins, superior sagittal sinus, right transverse sinus, and right internal jugular vein. The patient immediately started anticoagulation therapy with intravenous heparin infusion followed by daily oral rivaroxaban 10 mg. Follow-up imaging after 2 weeks showed resolution of the thrombosis, with recanalization of the cortical veins, superior sagittal sinus, right transverse sinus, and right internal jugular vein. She continued rivaroxaban therapy for 6 months, and remained well, without neurologic sequelae. A high level of concern for cerebral venous thrombosis may be important when treating active IBD patients, because anticoagulation treatment can prevent fatal complications.