This study aimed to evaluate the efficacy and safety between electromagnetic navigational bronchoscopy (ENB) and computed tomography (CT)-guided percutaneous localization before resection of pulmonary nodules. Pubmed, Embase, Web of Science, and the Cochrane Library databases were searched from January 1, 2000 to April 30, 2022, for relevant studies. Two reviewers conducted the search, selection, and extraction of data from eligible studies. The risk of bias was assessed using the Newcastle-Ottawa Scale. The primary outcome was the localization success rate, and the secondary outcomes were the pneumothorax incidence and localization time. The meta-analysis was performed by Review Manager 5.4. The protocol for the meta-analysis was registered on PROSPERO (Registration number: CRD42022345972). Five cohort studies comprising 441 patients (ENB group: 185, CT group: 256) were analyzed. Compared with the CT-guided group, the ENB-guided group was associated with lower pneumothorax incidence (relative ratio = 0.16, 95% confidence interval [CI]: 0.04-0.65, P = .01). No significant differences were found in location success rates (relative ratio = 1.01, 95% CI: 0.98-1.05, P = .38) and localization time (mean difference = 0.99, 95% CI: -5.73 to 7.71, P = .77) between the ENB group and CT group. Both ENB and CT-guided are valuable technologies in localizing lung nodules before video-assisted thoracoscopic surgery based on current investigations. ENB achieved a lower pneumothorax rate than the CT-guided group. In our opinion, there is no perfect method, and decision-making should be given the actual circumstances of each institute. Future prospective studies in the form of a randomized trial are needed to confirm their clinical value.