Introduction: Single-incision paediatric endosurgery is gaining popularity, especially for abdominal operations. However, few reports in the literature support the feasibility of uniportal thoracoscopic surgery for congenital lung malformations in paediatric patients. This paper presented the initial experience with uniportal thoracoscopic surgery and compared the surgical outcomes with multiport Video-Assisted Thoracoscopic Surgery (VATS) and traditional thoracotomy. Materials and Methods: From January 2009 to January 2018, a retrospective review of all patients (less than 18 years old) who underwent surgery for congenital lung malformations at our institution was performed. General data, operative data, anaesthesia parameters and surgical outcomes were collected. Results were analysed with one-way ANOVA and chi-square tests for continuous and categorical data. Results: Twenty-one patients with congenital lung malformations underwent surgery at our institution. The number of patients enrolled in thoracotomy, multiportal VATS and uniportal VATS groups was 8, 6 and 7, respectively. No difference in age, body weight, post-operative stay and drainage period was observed among the groups. A considerably high conversion rate (3/6, 50%) was observed in the multiportal VATS group. After the introduction of endobronchial blocker for one lung ventilation, all multi-portal and uniportal VATS procedures could be performed safely without residual lesion or mortality. Conclusions: VATS is feasible in the paediatric population, and it needs experienced surgical skills and unique anaesthetic requirements. For small infants with congenital lung malformations, uniportal VATS with endobronchial blocker is preferred.