Purpose <p>We evaluated the long-term outcomes of children undergoing thoracotomy lung resection for congenital lung malformations in terms of lung function, complications, and health-related quality of life (HRQOL).</p> Methods <p>We retrospectively reviewed 27 children who underwent thoracotomy at Osaka University Hospital (1992–2017) with at least five years of follow-up and postoperative lung function testing after six years of age. We compared the percent predicted vital capacity (%VC), percent predicted forced expiratory volume in 1&#xa0;s (%FEV₁), and FEV₁ to FVC ratio (FEV₁/FVC) as indicators of the lung function. Longitudinal changes in the lung function, pulmonary and musculoskeletal morbidities, and HRQOL were assessed using the Pediatric Quality of Life Inventory.</p> Results <p>%VC and FEV₁/FVC remained within the normal range but were significantly lower than the controls; %FEV₁ was below the normal range. No significant longitudinal changes in the lung function were observed. Asthma‑like symptoms appeared in 37.0% of the patients and persisted beyond adolescence. Musculoskeletal morbidities occurred in 33.3% of the patients, with five pectus excavatum cases requiring correction. HRQOL did not differ from that of the healthy controls.</p> Conclusions <p>In our study, children undergoing thoracotomy lung resection for congenital lung malformations exhibited a significantly lower lung function than the healthy controls, and these impairments persisted over an extended follow-up period. Long-term complications and a reduced lung function were not reflected in the subjective HRQOL.</p>