Background Esophageal atresia (EA) is a rare malformation with a wide range of co-morbidity and associated malformations impairing weight gain and growth. The aim of this study was to calculate specific percentiles for body weight and height for children born with esophageal atresia according to sex from birth to the age of 6 years, accounting for prematurity and presence of congenital heart disease (CHD). Methods Data was extracted from an anonymized voluntary national registry for patients born with esophageal atresia between 2001 and 2021, from birth until the age of six years. Missing values were imputed using a multiple imputation approach. In premature infants, chronological age was corrected for gestational week until the age of one year. The impact of sex and additional congenital heart disease on weight gain and growth was analysed using quartile regression models. Results In total, 1812 examinations of 485 patients were considered and 1232 examinations of 301 patients were finally included. Most data was available for children at birth and during the first year of life. Body weight was imputed for 3.3% and height for 12.5% of examinations. The mean body weight-for-age and length-for-age at birth according to gestational age was lower in EA patients and median body weight developed along the tenth percentile compared to the general population. Median height-for-age was at the 50th percentile during the first months of life, before crossing to lower percentiles before the age of one year. CHD had an additional negative impact on growth and weight gain, especially during the first year of life. Conclusions Children with EA had a reduced bodyweight and -height compared to the general population. Therefore, specific percentile curves are helpful to evaluate growth and development. Especially during the first year of life, particular attention is necessary and complications leading to a reduced calorie intake should be treated without delay to promote timely development and growth. Cardiac co-morbidities may further compromise weight gain in these patients, implying that such patients should be under even closer surveillance.