Upper limb ischemia presenting in neonatal period is extremely rare. Moreover, presenting newborn with evidence of intrauterine upper limb vascular occlusion is even rarer. It needs prompt intervention to restore perfusion and avoid morbidity. We present a newborn with right upper limb brachial artery thrombosis causing ischemia that was noted at birth and appeared later to be homozygous for factor V Leiden and glycoprotein IIIa with no other identifiable risk factors. In this report, we present the case, its successful medical management, proper counseling, and review of the literature. We recommend investigating the neonates and their parents for thrombophilia mutations when they present with unusual vascular occlusion site as newborns.