Objectives To explore whether multiparametric approach including blood oxygenation level-dependent MRI (BOLD-MRI) and intravoxel incoherent motion diffusion-weighted imaging (IVIM-DWI) can be applied in the assessment of renal function in children with chronic kidney disease (CKD). Materials and methods This prospective study included 74 children (CKD stage 1-3, 51; CKD stage 4-5, 12; healthy volunteers, 11) for renal MRI examinations including coronal T2WI, axial T1WI and T2WI, BOLD-MRI, and DWI sequences. We measured the renal cortex and medulla T2*, ADC, D-t, D-p, and f(p) values on BOLD and DWI images. Appropriate statistical methods were applied for comparing MRI-derived parameters among the three groups and calculating the correlation coefficients between MRI-derived parameters and clinical data. Receiver operating characteristic (ROC) curves were used to assess the diagnostic performance of MRI-derived parameters. Results There were significant differences in cortex T2*, ADC, D-t, f(p) and medulla T2*, ADC, D-t among the three groups. Cortex T2*, ADC, D-t, f(p) and medulla T2*, ADC, D-t had a trend: CKD stage 4-5 < CKD stage 1-3 < healthy volunteers. Cortex and medulla T2*, ADC, D-t were significantly correlated with eGFR, serum creatinine (Scr), cystatin C. In addition, cortex T2* and eGFR showed the highest correlation coefficient (r = 0.824, p < 0.001). Cortex D-t and medulla T2* were optimal parameters for differentiating healthy volunteers and CKD stage 1-3 or CKD stage 4-5 and CKD stage 1-3, respectively. Conclusions BOLD-MRI and IVIM-DWI might be used as a feasible method for noninvasive assessment of renal function in children with CKD.