Purpose: This study aimed to compare the diagnostic accuracy of [F-18]fluorodeoxyglucose (FDG) positron emission tomography (PET)/ magnetic resonance imaging (MRI) and [F-18]FDG PET/ computed tomography (CT) in tumor-node-metastasis staging of non-small-cell lung cancer. Methods: The study followed the Preferred Reporting Items for Systematic Reviews and Meta-Analyses for Diagnostic Test Accuracy (PRISMA-DTA) guidelines and retrieved all accessible studies from the Embase, PubMed, and Web of Science databases up to December 2022. Only studies in which both [F-18]FDG PET/MRI and [18F]FDG PET/CT were conducted on each individual patient were included. Two researchers independently extracted data on study characteristics and assessed the methodological quality using the Quality Assessment of Diagnostic Accuracy Studies (QUADAS-2) tool. Results: A total of 539 patients in eight studies were included in this analysis. For T staging, the pooled sensitivity of [F-18]FDG PET/CT was 0.90 (95% confidence interval [CI]: 0.81-0.96) and specificity of 0.97 (95% CI: 0.89-1.00), with corresponding values for [F-18]FDG PET/MRI of 0.88 (95% CI: 0.78-0.94) and 0.95 (95% CI: 0.87-0.99), respectively. For N staging, the pooled sensitivity of [F-18] FDG PET/CT was 0.70 (95% CI: 0.63-0.76), the specificity of 0.92 (95% CI: 0.88-0.95), and the area under the curve (AUC) was 0.90 (standard error [SE] = 0.06). The corresponding values for [F-18]FDG PET/MRI were 0.71 (95% CI: 0.65-0.77), 0.91 (95% CI: 0.87-0.94) and 0.88 (SE = 0.06), respectively. For M staging, the pooled sensitivity was 0.79 (95% CI: 0.62-0.91), the specificity was 0.94 (95% CI: 0.90-0.97), and AUC was 0.96 (SE = 0.03) for [F-18]FDG PET/CT. The corresponding values were 0.82 (95% CI: 0.70-0.91), 0.96 (95% CI: 0.93-0.98), and 0.94 (SE = 0.03), respectively, for [18F]FDG PET/MRI. Conclusions: According to the pooled data, [F-18]FDG PET/CT performed slightly better in terms of T staging than [F-18]FDG PET/MRI. In contrast, with regard to N staging and M staging the staging accuracy of both imaging techniques was comparable. To ensure that results are reliable, more high-level investigations will be required to assess these imaging modalities, in addition to optimized PET/MRI procedures.