Background: We performed a network meta-analysis to compare the diagnostic accuracy of contrast-enhanced ultrasound (CEUS) and shear wave elastography (SWE) in differentiating benign and malignant lesions in different body sites. Methods: A computerized literature search of Medline, Embase, SCOPUS, and Web of Science was performed using relevant keywords. Following data extraction, we calculated sensitivity, specificity, positive likelihood ratio (LR), negative LR, and diagnostic odds ratio (DOR) for CEUS, and SWE compared to histopathology as a reference standard. Statistical analyses were conducted by MetaDiSc (version 1.4) and R software (version 3.4.3). Results: One hundred and fourteen studies (15,926 patients) were pooled in the final analyses. Network meta-analysis showed that CEUS had significantly higher DOR than SWE (DOR = 27.14, 95% CI [2.30, 51.97]) in breast cancer detection. However, there were no significant differences between CEUS and SWE in hepatic (DOR = -6.67, 95% CI [-15.08, 1.74]) and thyroid cancer detection (DOR = 3.79, 95% CI [-3.10, 10.68]). Interestingly, ranking analysis showed that CEUS achieved higher DOR in detecting breast and thyroid cancer, while SWE achieved higher DOR in detecting hepatic cancer. The overall DOR for CEUS in detecting renal cancer was 53.44, 95% CI [29.89, 95.56] with an AUROC of 0.95, while the overall DOR for SWE in detecting prostate cancer was 25.35, 95% CI [7.15, 89.89] with an AUROC of 0.89. Conclusion: Both diagnostic tests showed relatively high sensitivity and specificity in detecting malignant tumors in different organs. Network meta-analysis showed that CEUS had higher diagnostic accuracy than SWE in detecting breast and thyroid cancer, while SWE had higher accuracy in detecting hepatic cancer. However, the results were not statistically significant in hepatic and thyroid malignancies. Further head-to-head comparisons are needed to confirm the optimal imaging technique to differentiate each cancer type.