Background Over the years the need for surgical treatment, timing of intervention, and the type of surgical approach have been discussed, but the treatment of congenital lung malformations remains controversial. The aim of this study was to compare the thoracotomy approach with the thoracoscopic technique by evaluating different surgical outcomes (duration of surgery, postoperative hospital stay, and complications). Methods All patients operated from January 2011 to March 2015 for suspected congenital cystic lung were included in the study. Patients treated for congenital lobar emphysema and tracheobronchial neoplasms were excluded from the study. Results In the analyzed period, 31 asymptomatic patients were treated: 18 lung resections were performed with thoracotomy (Group A) and 13 with the thoracoscopic approach (Group B). No significant differences were observed between the age and weight at surgery, length of the procedures, complications, and the need for postoperative intensive care between the two groups. The postoperative hospital stay in Group A was twice that for Group 2 (p = 0.0009). Conclusion Comparing thoracoscopic surgery with the traditional open approach, we confirmed the superiority of minimally invasive treatment in terms of postoperative hospital stay. Common technical recommendations can help pediatric centers to develop the thoracoscopic approach for the treatment of congenital pulmonary malformations.