Introduction: Surgery for congenital heart disease can generate cerebral perfusion-associated alterations with neurological repercussions. Objective: To analyze the relationship of peri-surgical cerebrovascular resistance index (RI) with mediate neurological functions after congenital heart disease surgery. Method: Prospective cohort study of 34 neonates in whom basilar artery RI, serum oxygen, carbon dioxide and lactate levels were determined before and after palliative or corrective procedures. We related pre-surgical RI with post-surgical ability to initiate the enteral route or to restore unassisted spontaneous breathing. Results: Three groups were formed: 79 neonates with high RI (> 0.73), 73 with normal RI (0.63 to 0.73) and eight with low RI (< 0.63). In the former group, high RI persisted in the postoperative period, with persistent hyperlactatemia and hypoxia; in 86 %, the enteral route could not be initiated, and neither could assisted ventilation be withdrawn. In the second group, RI remained within normal values. In the third group, although RI, serum lactate and arterial oxygen pressure tended to normalize, 71 % had severe neurological damage. Conclusions: RI changes were common, although neurological damage appears to occur more commonly when RI remains high, possibly associated with low cerebral blood flow.