Background Oxygen-uptake efficiency slope (OUES) is an objective measure of functional capacity that does not require a maximal effort but is considerably dependent on anthropometric variables and requires the generation of an appropriate reference value in children. This study aimed to establish normal reference values for OUES/kg in children with and without congenital heart diseases. Besides that, reference values are presented secondarily for OUES per body surface area (OUES/BSA). Design Cross-sectional. Methods Six hundred and seventy-six children and adolescents performed a maximal cardiopulmonary exercise test (305 healthy controls and 371 individuals with congenital heart defect), between four and 21 years old (481 males and 195 females, with a mean age of 12 years). Results The OUES reference value for the classification of children and adolescents with normal functional capacity (>80% of predicted maximum oxygen uptake) was 34.63 (sensitivity 77% and specificity 83%, p < 0.05). Regarding the body surface area, considering healthy patients and those with heart disease, the cutoff value of the OUES/BSA was 1151 with sensitivity of 79% and specificity of 79%. Conclusions OUES/kg may be an important marker tool in the differentiation between preserved or abnormal functional capacity in children and adolescents with and without congenital heart disease, even at the submaximal level of exercise.