Background Changes in renal microvascular perfusion are involved in several kidney diseases. Contrast-enhanced ultrasonography (CEUS) quantitative analysis can enable the estimation of renal microvascular perfusion non-invasively. However, to date, few pediatric patients with renal disease have been subjected to CEUS quantitative analysis. This study aimed to explore the feasibility of CEUS in evaluating renal microvascular perfusion in pediatric patients and paving its way to clinical practice. Methods Seventeen pediatric patients with chronic kidney disease (CKD) and five children without kidney disease were consecutively examined using CEUS. Quantitative analysis of CEUS images based on time-intensity curve (TIC) fittings was performed using specialized software. Quantitative parameters of wash-in microvascular blood flow, including A, k, B, and TtoPk, were generated from three regions of interest (ROIs) each in the cortex and medulla of each kidney. Results CEUS was performed in all children successfully and safely without the use of sedatives. All parameters (A, B, k, and TtoPk) demonstrated no statistical differences among the three sampling ROIs in the renal cortex and medulla. All parameters (A, B, k, and TtoPk) showed no statistical differences between the left and right sides of kidneys both in cortices and medullas. Comparing with patients with CKD stage 3-5, both control group and patients with CKD stage 1-2 had significantly higher values of parameter A in the renal cortex (p = 0.025 and p = 0.031, respectively). In control group and patients stage 1-2, the values of parameters k in the renal cortices were significantly higher than that in the renal medullas, while in patients with CKD stage 3-5, parameter k showed no statistically significant differences between the renal cortex and medulla (p = 0.173). Conclusion CEUS is safe and practicable in pediatric patients with chronic kidney disease. Renal microvascular perfusion estimated by CEUS could be a robust approach in the evaluation of pediatric renal diseases. Parameters A and k derived from CEUS quantitative analysis can provide great potential in non-invasive assessment of renal microvascular perfusion impairment in pediatric CKD.