Ventricular assist device (VAD) use in children has increased dramatically. There are currently few data regarding trends in anticoagulation management for pediatric VADs. A retrospective cohort study was conducted for patients with an International Classification of Diseases, Ninth Revision (ICD-9) code for VAD implantation from 2000 to 2011 from the Pediatric Health Information System database. Patient demographics, use of extracorporeal membrane oxygenation, orthotopic heart transplantation (OHT), disease states, and medications pertinent to the management of VAD anticoagulation were queried. Patients were grouped into 3 year time periods to evaluate trends in medication use over time. Four hundred sixty-six patients were identified with a median length of VAD therapy of 21 days (range 1-362 days). In-hospital mortality was 31.9%, and 54.5% underwent OHT. Length of VAD therapy and patients undergoing OHT increased, while mortality decreased. Patients received a median of two anticoagulant medications (range 0-6), one (range 0-4) antiplatelet medications, three (range 0-5) procoagulant medications, and one (range 0-3) antifibrinolytics. Patients received greater mean numbers of anticoagulant, procoagulant, antifibrinolytic, and antiplatelet agents, and the use of oral medications increased more than twofold over time. There is wide variability for in-hospital pediatric VAD anticoagulation management, with a significant increase in the use of oral agents in more recent years.