Cerebral venous sinus thrombosis is a rare but serious cause of headache. In this report, we present a young man with poorly controlled Crohn's disease who presented with a 2-week history of headache and fluctuating left-sided sensory and motor symptoms. CT demonstrated changes consistent with either a subarachnoid haemorrhage or venous sinus thrombosis. The ensuing magnetic resonance venogram confirmed superior sagittal venous sinus thrombosis and an infarct of his right superior frontal lobe. The patient was started on low-molecular weight heparin and steroids. He required multi-disciplinary input from the stroke physicians, neurologists, gastroenterologists, dieticians and physiotherapists. He made a full neurological recovery and is now on long-term azathioprine. The purpose of this report is to highlight the consideration of venous sinus thrombosis in the diagnosis of headache and as a rare extraintestinal complication of Crohn's disease.