Although application of intraoperative computer navigation technique had been integrated into placement of pedicle screws (PSs) in thoracic fusion for years, its security and practicability remain controversial. The aim of this study is to evaluate the accuracy, the operative time consumption, the amount of intraoperative blood loss, time of pedicle insertion and the incidence of complications of thoracic pedicle screw placement in patients with thoracic diseases such as scoliosis and kyphosis. Pubmed, Web of Knowledge, and Google scholar were searched to identify comparative studies of thoracic pedicle screw placement between intraoperative computer navigation and fluoroscopy-guided navigation. Outcomes of malposition rate, operative time consumption, insertion time, intraoperative blood loss, and the incidence of complications are evaluated. Fourteen articles including 1723 patients and 9019 PSs were identified matching inclusion criteria. The malposition rate was lower (RR: 0.33, 95 % CI: 0.28-0.38, P < 0.01) in computer navigation group than that in fluoroscopy-guided navigation group; the operative time was significantly longer [weighted mean difference (WMD) = 23.66, 95 % CI: 14.74-32.57, P < 0.01] in computer navigation group than that in fluoroscopy-guided navigation group. The time of insertion was shorter (WMD = -1.88, 95 % CI: -2.25- -1.52, P < 0.01) in computer navigation group than that in fluoroscopy-guided navigation group. The incidence of complications was lower (RR = 0. 23, 95 % CI: 0.12-0.46, P < 0.01) in computer navigation group than that in the other group. The intraoperative blood loss was fewer (WMD = -167.49, 95 % CI: -266.39- -68.58, P < 0.01) in computer navigation group than that in the other. In conclusion, the meta-analysis of thoracic pedicle screw placement studies clearly demonstrated lower malposition rate, less intraoperative blood loss, and fewer complications when using computer navigation. This result provides strong evidence that computer technology could be safer and more reliable than fluoroscopy-guided navigation.