Aim This systematic review and meta-analysis was carried out to compare the diagnostic accuracy of Magnetic resonance elastography (MRE) and Fibroscan for detecting liver fibrosis in Chronic Hepatitis B (CHB) patients. Methods The PubMed, the Cochrane Library, and the Web of science databases were searched for studies that evaluated the diagnostic value of MRE and Fibroscan for liver fibrosis in CHB patients until March 1st 2017. The quality of the included studies was assessed by the revised Quality Assessment for Studies of Diagnostic Accuracy tool (QUADAS-2). Meta-disc 4.1 was used to summary the area under receiver operating characteristics curve (AUROC), sensitivity, specificity, diagnostic odds ratios to assess the accuracy of staging liver fibrosis using MRE and Fibroscan. Results A total of nine MRE studies with 1470 patients and fifteen Fibroscan studies with 3641 patients were included in this systematic review. The summary AUROC values using MRE and Fibroscan for detecting significant fibrosis, advanced fibrosis and cirrhosis were 0.981 vs. 0.796(p < 0.001), 0.972 vs. 0.893(p < 0.001), and 0.972 vs. 0.905 (p < 0.001). The pooled sensitivity and specificity using MRE for the diagnosis of significant fibrosis, advanced fibrosis and cirrhosis were 92.8% and 93.7%, 89.6% and 93.2%, 89.5% and 92.0%, respectively. The pooled sensitivity and specificity using Fibroscan for the diagnosis of significant fibrosis, advanced fibrosis and cirrhosis were 71.6% and 81.6%, 79.0% and 84.6%, 80.0% and 86.6%, respectively. Conclusion MRE is more accurate than Fibroscan in diagnosing liver fibrosis in CHB patients, especially in diagnosing significant fibrosis and advanced fibrosis.