Background In 10-15% of children with esophageal atresia (EA) delayed reconstruction of esophageal atresia (DREA) is necessary due to long-gap EA and/or prematurity/low birth weight. They represent a patient subgroup with high risk of complications. We aimed to evaluate postoperative morbidity and health-related quality of life (HRQOL) in a Swedish national cohort of children with DREA. Methods Postoperative morbidity, age-specific generic HRQOL (PedsQLTM 4.0) and condition-specific HRQOL (The EA-QOL questionnaires) in children with DREA were compared with children with EA who had primary anastomosis (PA). Factors associated with the DREA group’s HRQOL scores were analyzed using Mann-Whitney U-test and Spearman’s rho. Clinical data was extracted from the medical records. Significance level was p<0.05.Results Thirty-four out of 45 families of children with DREA were included and 30 returned the questionnaires(n=8 children aged 2-7 years; n=22 children aged 8-18 years). Compared to children with PA(42 children aged 2-7 years; 64 children aged 8-18 years), there were no significant differences in most early postoperative complications. At follow-up, symptom prevalence in children aged 2-7 with DREA ranged from 37.5% (heartburn) to 75%(cough). Further digestive and respiratory symptoms were present in ≥50%. In children aged 8-18, it ranged from 14.3%(vomiting) to 40.9%(cough), with other digestive and airway symptoms present in 19.0-27.3%. Except for chest tightness(2-7 years), there were no significant differences in symptom prevalence between children with DREA and PA, nor between their generic or condition-specific HRQOL scores(p>0.05). More children with DREA underwent esophageal dilatations (both age groups), gastrostomy feeding(2-7 years), and antireflux treatment (8-18 years), p<0.05. Days to hospital discharge after EA repair and a number of associated anomalies showed a strong negative correlation with HRQOL scores (2-7 years). Presence of cough, airway infection, swallowing difficulties and heartburn were associated with lower HRQOL scores (8-18 years), p<0.05. Conclusions Although children with DREA need more treatments, they are not a risk group for postoperative morbidity and impaired HRQOL compared with children with PA. However, those with a long initial hospital stay, several associated anomalies and digestive or respiratory symptoms risk worse HRQOL. This is important information for clinical practice, families and patient stakeholders.