With advancements in cardiopulmonary rehabilitation over the past few decades, the survival rate of patients with congenital heart disease (CHD) has increased. However, the Cardiopulmonary fitness (CPF) of these patients is poor. Here, we aimed to investigate CPF in preschoolers with CHD (aged 4 to 6 years) using cardiopulmonary exercise testing. We retrospectively compared 102 healthy preschoolers with 80 preschoolers with CHD. The latter had lower peak oxygen consumption, oxygen consumption at anaerobic threshold and metabolic equivalent at anaerobic threshold. The same result was observed in boys with CHD, but not in girls, when sex was sub-analyzed. Considering the body composition, children with CHD had a lower fat-free mass index (FFMI) than their healthy peers. Healthy preschoolers with a normal body mass index (BMI) had higher anaerobic threshold and peak metabolic equivalent values than overweight or underweight children. This was categorized under the BMI reference of the Ministry of Health and Welfare in Taiwan. In conclusion, the CPF difference between the CHD and healthy groups was identified as early as in preschool age, and better CPF in healthy preschoolers within the normal BMI range suggests the importance of weight control in young children.