Acute kidney injury (AKI) is a frequent complication after cardiopulmonary bypass surgery during infancy. Standard methods for evaluating renal function are not particularly sensitive nor are proximate indicators of renal dysfunction that allow intervention in real time. Near-infrared spectroscopy (NIRS) is a newer noninvasive technology that continuously evaluates regional oximetry and may correlate with renal injury and adverse outcomes after cardiac surgery in infants. This prospective observational study enrolled 40 infants (age, <12 months) undergoing biventricular repair. Continuous renal oximetry data were collected for the first 48 postoperative hours and correlated with postoperative course, standard laboratory data, and the occurrence of acute renal injury. Subjects with low renal oximetry (below 50% for >2 h) had significantly higher postoperative peak creatinine levels by 48 h (0.8 ± 0.4 vs. 0.52 ± 0.2; p = 0.003) and a higher incidence of AKI (50 vs. 3.1%; p = 0.003) than those with normal renal oximetry. These subjects also required more ventilator days and greater vasoactive support, and they had elevated lactate levels. Prolonged low renal near-infrared oximetry appears to correlate with renal dysfunction, decreased systemic oxygen delivery, and the overall postoperative course in infants with congenital heart disease undergoing biventricular repair.