Pediatric studies have found a correlation between the clinical heart failure score and N-terminal pro-brain natriuretic peptide (NT-proBNP) levels. However, the clinical usefulness of this marker remains unclear in neonates. At hospitals without pediatric cardiologists, neonatologists or general pediatricians must judge whether surgery is indicated and transfer patients to a specialized hospital in a timely fashion as required. Thus, we tested the hypothesis that increased NT-proBNP levels predict short-term outcomes in neonates with congenital heart diseases (CHDs) and are thus a useful tool for evaluating clinical status and guiding treatment. Subjects were term or near-term newborns (≥36 weeks' gestation) with CHDs confined to left-to-right shunt lesions. Clinical parameters and NT-proBNP levels were measured on the first 7, 14, 21, and 28 days of life (DOL). We divided patients into a surgical (n = 7) and a conservative-treatment group (n = 21), and then compared clinical variables and outcomes between the groups. In the surgical group, NT-proBNP levels had a tendency to increase during the first 14 postnatal days and were significantly greater than in the conservative-treatment group on 7 DOL [median (range), 13,983 pg/mL (4,732-26,524) vs. 1,954 pg/mL (671-10,881); p = 0.0028] and on 14 DOL [29,274 pg/mL (14,006-33,740) vs. 2,050 pg/mL (1,304-9,250); p = 0.0055]. In contrast, NT-proBNP levels tended to decrease sequentially in the conservative-treatment group. The values of additional markers, such as mean NT-proBNP level on 7 and 14 DOLs (M7-14) and NT-proBNP level on 14 DOL minus that on 7 DOL (Δ7-14), were both significantly greater in the surgical group than in the conservative-treatment group. To examine the usability of M7-14 and Δ7-14 when the difference and mean cut-off levels were set at 10,000 and 3,000 pg/mL, respectively, the sensitivity and specificity were both 100 %. In neonates who had CHDs with left-to-right shunt, analysis of the association between clinical variables and short-term outcomes showed that NT-proBNP, especially M7-14 and Δ7-14, is a useful predictor of early surgery.