We employ a hybrid diffuse correlation spectroscopy (DCS) and near-infrared spectroscopy (NIRS) monitor for neonates with congenital heart disease (n=33). The NIRS-DCS device measured changes during hypercapnia of oxyhemoglobin, deoxyhemoglobin, and total hemoglobin concentrations; cerebral blood flow (rCBF(DCS)); and oxygen metabolism (rCMRO(2)). Concurrent measurements with arterial spin-labeled magnetic resonance imaging (rCBF(ASL-MRI), n=12) cross-validate rCBF(DCS) against rCBF(ASL-MRI), showing good agreement (R=0.7, p=0.01). The study demonstrates use of NIRS-DCS on a critically ill neonatal population, and the results indicate that the optical technology is a promising clinical method for monitoring this population.