Abstract Background The aim of this study was to assess surgical intervention strategies for congenital cystic lesions of the lungs (CCL), focusing on the safety of lung resection. Materials and methods The clinical features of 27 children (CCAM, n = 16; bronchial atresia, n = 4; bronchogenic cyst, n = 3; pulmonary sequestration, n = 3; lobar emphysema, n = 1) who were treated at our institution between 1995 and 2014 were analyzed. Results Of the 27 patients, 14 were asymptomatic, and 13 were symptomatic. The youngest symptomatic patient presented with pneumonia at 9 months of age. The mean age at surgery was 4 months in the asymptomatic group and 4.1 years in the symptomatic group. The mean operating time was 167 minutes in the asymptomatic group and 275 minutes in the symptomatic group (P < 0.001). The mean amount of intraoperative bleeding was 15 g in the asymptomatic group and 83.4 g in the symptomatic group (P < 0.05). All of the prenatally diagnosed patients underwent surgery within six months of birth. Three patients had remnant cystic lesions, all of which involved cystic lesions located over the lobulation anomalies of the lung. Conclusions To minimize surgical invasiveness, surgery for CCL should be performed during the asymptomatic period or within six months after birth.