Background The purpose of this study was to assess the safety issues concerning anesthetic management of video-assisted thoracoscopic surgery (VATS) in pediatric patients. Methods The medical records of 52 pediatric patients undergoing VATS using general anesthesia and one-lung ventilation (OLV) were reviewed. OLV was achieved with a Fogarty catheter (n = 23) or endobronchial intubation (n = 7) in patients < 10 years of age (group Y, n = 30), and using a double-lumen tube (n = 19) or a univent (n = 3) in children aged between 10 and 16 years of age (group O, n = 22). Hypoxemia, hypercarbia, the difference between ETCO2 and PaCO2, and the effect of CO2 insufflation were assessed. Results A decrease in SpO2 less than 90% was observed in 40% of the group Y, compared to none of the group O (P < 0.05). A hypercarbia (ETCO2 > 50 mmHg) was observed more frequently in group Y (40%) than in group O (0%; P < 0.05). The difference between the ETCO2 and PaCO2 was 10.4 ± 8.9 mmHg in group Y and 4.6 ± 3.9 mmHg in group O (P < 0.05). Hypercarbia and acidosis occurred more frequently in patients with CO2 insufflation than those without insufflation in group Y. Conclusions Although the anesthesia for VATS in pediatric patients was successfully accomplished, the infants and younger children presented with more intra-operative problems when compared with older children. The anesthetic management for VATS in infants and younger children requires careful and vigilant monitoring.