Objective To compare the short-term outcomes of small thoracotomy and thoracoscopic approach for pediatric lobectomy. Methods From June 2011 to June 2016, 42 patients with lung diseases undertook lobectomy in Xinhua Hospital. There were 24 males and 18 females with an average age of 7.13±5.00 years, ranging from 4 months to 16 years. According to different operation methods, they were divided into a thoracoscopy group (n=22) and a small incision group (n=20). Duration of operation, intraoperative blood loss, duration of postoperative drainage, and postoperative hospital stay and complications between the two groups were recorded and compared. Results There was no significant difference in the age, body weight between the two groups (8.44±4.99 yearsvs. 5.68±4.69 years,t=1.84,P=0.07; 34.18±16.52 kgvs. 25.03±18.06 kg,t=1.72,P=0.09). Two patients (9%) undergoing thoracoscopy required conversion to small thoracotomy. Perioperative outcomes, including operation time (151.64±74.59 minvs. 136.40±50.36 min,t=0.77,P=0.45), intraoperative blood loss (43.41±45.91 mlvs. 79.50±131.00 ml,t=–1.21,P=0.23), drainage duration (5.00±1.79 dvs. 4.90±2.36 d,t=0.23,P=0.82), length of hospital stay (8.41±3.11 dvs. 8.65±2.66 d,t=–0.27,P=0.79) showed no significant differences between the two groups. One patient suffered pneumonia in thoracoscopy group after operation and the rest patients recovered well without severe complications such as atelectasis, active bleeding and bronchopleural fistula. Conclusion Lobectomy via small thoracotomy and thoracoscopic approach is effective and safe for pediatric patients with equivalent short-term outcomes. While thoracoscopic surgery with relatively small incision achieves good cosmetic outcome.