Internal jugular vein thrombosis is a rare but treatable disorder with most of the reports in the literature related to the adult population. The most common reported cause is iatrogenic trauma to the internal jugular vein and only a few cases have been reported in the paediatric population. We present a case of bilateral internal jugular venous thrombosis with pulmonary and cerebral complications in a 14-year-old girl with protein S deficiency. This problem has not been previously reported in the world literature.