Little is known about the impact of preoperative location on outcomes in infants undergoing cardiac surgery for congenital heart disease. This study was designed to evaluate the morbidity and mortality among infants who were cared for in a neonatal ICU (NICU) versus dedicated cardiovascular intensive care unit (CVICU) prior to cardiac surgery in a multi-institutional population. Data were obtained from a multicenter, administrative, national dataset, Pediatric Health Information System (PHIS). Patients 0 to 45 days undergoing surgery for congenital heart disease (with or without cardiopulmonary bypass) at a PHIS-participating hospital (2004 to 2013) were included. Propensity score matching was performed to match the NICU and the CVICU patients with similar demographic and preoperative clinical characteristics. A total of 5,376 patients from 20 hospitals met inclusion criteria. By propensity score matching, 2,456 patients matched 1 to 1 between the NICU and the CVICU groups. Outcomes including mortality (NICU vs CVICU, 11.9% vs 8.8%, p < 0.001), preoperative and total hospital length of stay (LOS), and total length of mechanical ventilation were significantly greater among the NICU patients compared with the CVICU patients. There was no significant difference in mortality among the patients undergoing "low" complexity operations (NICU vs CVICU, 8.4% vs 6.7%, p = 0.22), and patients undergoing treatment at high volume hospitals (NICU vs CVICU, 9.6% vs 9.5%, p = 0.95). This study demonstrates that preoperative location might impact outcomes in children undergoing operation for congenital heart disease. It is possible that preoperative location may be surrogate for other factors that may bias the results. Further study is warranted.