© 2018 Annals of Pediatric Cardiology | Published by Wolters Kluwer-Medknow. Thrombosis and systemic embolization are important complications of extracorporeal membrane oxygenation (ECMO). We present a 2.5 kg neonate born at 37.4 weeks with hypoplastic left heart supported on ECMO that developed an acute, occlusive distal aortic thrombus that was emergently managed by transcatheter Angiojet® (Boston Scientific, Boston, MA) thrombectomy. The procedure successfully restored perfusion to the lower extremities with sustained result upon 1-week follow-up. This case highlights the Angiojet® thrombectomy as a treatment option for limb-or organ-threatening acute thrombus in even the most complex ECMO patients.