Early skin-to-skin contact (SSC), beginning in the delivery room, provides myriad health benefits for mother and baby. Early SSC in the delivery room is the standard of care for healthy neonates following both vaginal and cesarean delivery. However, there is little published evidence on the safety of this practice in infants with congenital anomalies requiring immediate postnatal evaluation, including critical congenital heart disease (CCHD). Currently, the standard practice following delivery of infants with CCHD in many delivery centers has been immediate separation of mother and baby for neonatal stabilization and transfer to a different hospital unit or a different hospital altogether. However, most neonates with prenatally diagnosed congenital heart disease, even those with ductal-dependent lesions, are clinically stable in the immediate newborn period. Therefore, we sought to increase the percentage of newborns with prenatally diagnosed CCHD who are born in our regional level II–III delivery hospitals who receive mother-baby SSC in the delivery room. Using quality improvement methodology, through a series of Plan-Do-Study-Act cycles we successfully increased mother-baby skin-to-skin contact in the delivery room for eligible cardiac patients born across our city-wide delivery hospitals from a baseline 15% to greater than 50%. Supplementary Information The online version contains supplementary material available at 10.1007/s00246-023-03149-2.