Background This study evaluated the efficacy and safety of oral triiodothyronine (T3; Tetronine, Dalim BioTech, Korea) for infants and children undergoing cardiopulmonary bypass in an Indonesian population. Methods We performed a single-center, randomized, double-blind, and placebo-controlled trial in children aged 3 years and younger undergoing congenital heart disease operations with cardiopulmonary bypass. We administered oral T3 (1 μg/kg per body weight/dose) or placebo (saccharum lactis) by nasogastric tube every 6 hours for 60 hours after induction of anesthesia. The primary end point, time to extubation, was compared with Cox regression. Results The modified intention-to-treat group included 101 placebo and 104 treated patients. The stratified log-rank test did not show a significant treatment difference (p = 0.061) for time to extubation, but after adjustment for age, the nutritional Z score, and Aristotle surgical complexity, the hazard ratio was 1.33 (95% confidence interval, 1.00 to 1.76; p = 0.049). The effect of T3 was stronger in the strata aged 5 months and younger (hazard ratio, 1.86; 95% confidence interval 1.02 to 3.39; p = 0.043). Median intubation time was 47.3 hours for the placebo and 32.1 hours for the T3 group in aged 5 months and younger. Adverse events rates, including arrhythmia, were similar between groups, although sepsis was more frequent with placebo. Conclusions Oral T3 supplementation may shorten time to extubation in children undergoing congenital heart disease operations, particularly infants aged 5 months or younger. Administration is relatively safe, simple and inexpensive.