Infective endocarditis (IE) in the pediatric population can present as a life-threatening condition. Optimal timing for surgical intervention should consider surgical risks versus the risk of neurologic complications. We herein report our experience with this group of critically ill children. Retrospective analysis of patient charts of all patients who underwent urgent surgical treatment of aortic IE from 1994 to 2014 was performed. Nine patients with acute storming IE of the aortic valve or the ascending aorta were urgently operated (eight normal heart, one congenital aortic stenosis), age ranged from 8 weeks to 4.2 years. Causative organisms were Staphylococcus aureus (2), Staphylococcus coagulase negative (1), Kingella kingae (2), Streptococcus pneumoniae (2), or culture negative (2). Presenting symptoms other than hemodynamic instability were neurologic decompensation (5) coronary embolization (1) and cardiogenic shock due to scalded skin syndrome (1). CT and MRI demonstrated significant brain infarcts in four patients. Operations performed were the Ross operation (7) and ascending aortic reconstruction (2). There were no operative deaths. At a median follow-up of 6 years (range 2–196 months), all patients are alive and well. Re-intervention included homograft replacement (2) and transcatheter Melody valve implantation (1). At their last follow-up, the neo-aortic valve was functional in all patients with minimal regurgitation and all had full resolution of the neurological deficits. Urgent surgical treatment for aortic valve IE in infants is challenging. Although surgery is complex and pre-disposing conditions such as sepsis, neurologic and cardiac decompensations are prevalent, operative results are excellent and gradual and significant neurologic improvement was noted over time.