Heparin-induced thrombocytopenia (HIT) is rare in the pediatric population, with a majority occurring in the pediatric intensive care unit setting. All cases reported to date have been associated with the use of unfractionated heparin. Because unfractionated heparin is the anticoagulant of choice for extracorporeal membrane oxygenation (ECMO) and other extracorporeal therapies, the development of HIT in these patients can be devastating, making management problematic. We report a case of HIT type II with evidence of small-vessel arterial thrombosis in a 17-month-old boy receiving ECMO and continuous renal replacement therapy successfully treated with argatroban.