Ulcerative colitis (UC) is a rare cause of cerebral sinus thrombosis. We describe a 10-year-old patient with UC who developed cerebral sinus thrombosis during an acute exacerbation of his colitis and was found to be heterozygous for factor V Leiden. He was successfully treated with enoxaparin. Enoxaparin was then used for prophylaxis during acute exacerbations of his UC without any recurrence/progression of cerebral venous thrombosis. This report describes a cerebral thrombotic event in a child with UC and factor V Leiden.