Patients with inflammatory bowel disease (IBD) are at higher risk of venous thrombosis than the general population, with thromboembolism being a recognized extraintestinal manifestation. Although thrombotic events typically present as deep vein thrombosis and pulmonary embolism, other presentations are possible. Cerebral venous sinus thrombosis (CVST) is a relatively rare example associated with high morbidity and a mortality rate of 50% when misdiagnosed or the diagnosis is delayed. Despite this, CVST is a reversible complication with favorable outcomes when diagnosed early and treated appropriately. In this report, we present a case of cerebral sinus thrombosis in a 35-year-old female during a relapse of ulcerative colitis. During the relapse of ulcerative colitis, CVST manifested with a seizure, focal neurological deficit, and altered mental status. After blood workup, magnetic resonance imaging (MRI), and venography, the diagnosis of CVST was confirmed. We immediately started the patient on low-molecular-weight heparin, and during a six-month follow-up period, she made a full recovery with recanalization of the thrombosis on imaging. Despite CVST being a fatal complication of IBD, our report and data in the literature indicate that full remission is possible when it is correctly diagnosed and treated.