Low cardiac output syndrome (LCOS) and maximum vasoactive inotropic score (VIS) have been used as surrogate markers for early postoperative outcomes in pediatric cardiac surgery. The objective of this study was to determine the associations between LCOS and maximum VIS with clinical outcomes in neonatal cardiac surgery. This was a secondary retrospective analysis of a prospective randomized trial, and the setting was a pediatric cardiac intensive care unit in a tertiary care children’s hospital. Neonates (n = 76) undergoing corrective or palliative cardiac operations requiring cardiopulmonary bypass were prospectively enrolled. LCOS was defined by a standardized clinical criteria. VIS values were calculated by a standard formula during the first 36 postoperative hours, and the maximum score was recorded. Postoperative outcomes included hospital mortality, duration of mechanical ventilation, intensive care unit (ICU) and hospital lengths of stay (LOS), as well as total hospital charges. At surgery, the median age was 7 days and weight was 3.2 kg. LCOS occurred in 32 of 76 (42%) subjects. Median maximum VIS was 15 (range 5–33). LCOS was not associated with duration of mechanical ventilation, ICU LOS, hospital LOS, and hospital charges. Greater VIS was moderately associated with a longer duration of mechanical ventilation (p = 0.001, r = 0.36), longer ICU LOS (p = 0.02, r = 0.27), and greater total hospital costs (p = 0.05, r = 0.22) but not hospital LOS (p = 0.52). LCOS was not associated with early postoperative outcomes. Maximum VIS has only modest correlation with duration of mechanical ventilation, ICU LOS, and total hospital charges.