Background Undernutrition is a common problem among children with congenital heart disease (CHD) and may lead to poorer surgical outcomes. A higher intake of energy during the postoperative period of CHD surgery seems to be associated with better outcomes. This study aimed to investigate the effect of the use of energy‐enriched formula (EE‐formula) compared with normocaloric formula during 30 days after CHD surgery. Methods A randomized controlled trial with patients undergoing heart surgery in a tertiary hospital in southern Brazil from March 2017 to December 2017 was performed. The intervention group received EE‐formula (1 kcal/mL), and the control group received normocaloric formula (0.67 kcal/mL). The researcher in charge of anthropometric evaluation was blinded to the randomization. Results Fifty‐nine patients were included; 30 in control group and 29 in intervention group. There were no statistically significant differences between groups regarding age, gender, anthropometry, and surgical risk classification after randomization. A statistically significant difference in z‐score of weight for age and in weight gain variation rate between groups after intervention was observed. Antibiotic use was less frequent in the intervention group, and hospital length of stay was shorter. General gastrointestinal side effects were similar between groups, whereas diarrhea was more frequent in the intervention group. However, this side effect was limited and had spontaneous resolution in 4 out of 6 cases. Conclusion This study demonstrates that EE‐formula use after heart surgery of patients with CHD is well tolerated and may improve short‐term nutrition outcome, decrease hospital stay, and reduce antibiotic use.