Background The differential diagnosis of cystic renal masses still faces great challenges. There has been no systematically assessment to compare the value of contrast-enhanced ultrasound (CEUS) with magnetic resonance imaging (MRI) in the diagnosis of cystic renal masses. Purpose To perform a meta-analysis to compare the diagnostic efficacy of CEUS with that of MRI for cystic renal masses. Material and Methods A systematic search was performed for literature evaluating the diagnostic performance of CEUS or MRI in cystic renal masses. Quality assessment of diagnostic studies 2 (QUADAS-2) was used to evaluate the quality of each study included. The pooled sensitivity, specificity, positive likelihood ratio, negative likelihood ratio, and the areas under the summary receiver operating characteristic (AUCs-SROC) curve for CEUS and MRI were calculated, respectively. Results Seventeen studies with 1142 lesions were included. The pooled sensitivity, specificity, positive likelihood ratio, and negative likelihood ratio for CEUS /MRI were 0.95/0.92, 0.84/0.91, 5.62/6.74, and 0.09/0.13, respectively. The AUCs-SROC curves for the two methods were 95.66% and 94.65%. The subgroup analysis indicated that the scanning slice thickness may influence the diagnostic efficacy of MRI. Conclusion Both CEUS and MRI have good diagnostic performance for cystic renal masses and can provide the reference for clinicians. CEUS is more sensitive but less specific than MRI.