Background: Recently, accumulating evidences have revealed that microRNA-106 (miR-106) may serve as a non-invasive and cost-effective biomarker in gastric cancer (GC) detection. However, inconsistent results have prevented its application to clinical practice. Methods: As a result of this, a comprehensive meta-analysis was conducted to evaluate the diagnostic performance of miR-106 alone and miR-106-related combination markers for GC detection. Meanwhile, an integrative bioinformatics analysis was performed to explore the function of miR-106 at the systems biology level. Results: The results in our work showed that sensitivity of 0.71 (95% CI 0.65-0.76) and specificity of 0.82 (0.72-0.88), with the under area AUC (area under the curve) value of 0.80 (0.76-0.83) for miR-106 alone. Prospectively, miR-106-related combination markers improved the combined sensitivity, specificity and AUC, describing the discriminatory ability of 0.78 (0.65-0.87), 0.83 (0.77-0.89) and 0.88 (0.85-0.90) in the present analysis. Furthermore, targets of miR-106 were obtained and enriched by gene ontology and Kyoto Encyclopedia of Genes and Genomes pathway analysis, revealing their associations with the occurrence and development of GC. Hub genes and significant modules were identified from the protein-protein interaction networks constructed by miR-106 targets and found closely associated with the initiation and progression of GC again. Conclusions: Our comprehensive and integrative analysis revealed that miR-106 may be suitable as a diagnostic biomarker for GC while microRNA combination biomarkers may provide a new alternative for clinical application. However, it is necessary to conduct large-scale population-based studies and biological experiments to further investigate the diagnostic value of miR-106.