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Inflammatory bowel disease (IBD) is a well-recognized risk factor for thrombotic events in adults but data on children are scarce. In the great majority of adult patients, thrombotic events are usually deep vein thrombosis and pulmonary embolism. Other sites such as jugular veins are extremely rare. We present a case of Lemierre syndrome in an adolescent girl with active ulcerative colitis and discuss possible risk factors. This is the first reported case of severe Lemierre syndrome with thrombus extension to cranial veins in a patient with ulcerative colitis. Early recognition of Lemierre syndrome in patients who present with rapidly worsening symptoms of neck pain, fever and signs of pharyngitis is imperative because it increases a chance of favorable prognosis. It is important for pediatricians treating IBD patients not to underestimate possible thrombotic events in children with IBD. Recognition of additional risk factors is crucial for prompt diagnosis and adequate treatment.