The optimal myocardial protection strategy for newborns/infants undergoing congenital heart surgery remains controversial. The purpose of this study was to compare myocardial protection using histidine-tryptophan-ketoglutarate (HTK) and cold blood cardioplegia in a neonatal piglet model. Twenty-one piglets were randomized to three groups: the control group (C group, n = 7), a single dose of HTK group (H group, n = 7), and multidose cold blood cardioplegia group (B group, n = 7). Animals in the two experimental groups were placed on hypothermic cardiopulmonary bypass, after which the ascending aorta was clamped for 2 hours. Immediately after declamping, both the difference between arterial and coronary sinus blood lactate concentrations and the oxygen extraction did not differ between the H group and the B group. At 3 hours after declamping, rise in serum troponin-T and creatine kinase isoenzyme MB levels showed no significant differences between the H group and the B group (p = 0.735 and p = 0.103, respectively). No significant differences were noted in the myocardial lactate content, ATP content, and histopathological score between the H group and the B group (p = 0.810, p = 0.158, and p = 0.399, respectively). Transfusion requirement in the B group was significantly more than that in the H group (p = 0.003). HTK solution provides equivalent myocardial protection to multidose cold blood cardioplegia for the neonatal heart with less transfusion requirement.