The perfusion index (PI) is a non-invasive method to assess peripheral perfusion, derived from and displayed by pulse oximeters. While pulse oximetry demonstrates moderate sensitivity in detecting obstructive left heart lesions, including coarctation of the aorta (CoA), its limitations underscore the need for improved screening techniques. This report presents the cases of two full-term neonates diagnosed with CoA, highlighting the role of PI in early detection before clinical signs such as pulse discrepancies and blood pressure gradients become apparent. Both neonates exhibited abnormal PI readings (low post-ductal PI and a significant pre- to post-ductal PI differential) prior to the emergence of traditional diagnostic signs of CoA. Both patients were treated with prostaglandin E1 and underwent corrective surgery. Although further research is required and PI is not yet recommended as a standard screening parameter for congenital heart defects, monitoring microcirculation through PI shows promise for earlier detection of left heart obstructive defects like CoA.