Abstract Objectives To address SPECT’s radioactivity, complexity, and costliness in measuring renal function, this study employs artificial intelligence (AI) with non-contrast CT to estimate single-kidney glomerular filtration rate (GFR) and split renal function (SRF). Methods 245 patients with atrophic kidney or hydronephrosis were included from two centers (Training set: 128 patients from Center I; Test set: 117 patients from Center II). The renal parenchyma and hydronephrosis regions in non-contrast CT were automatically segmented by deep learning. Radiomic features were extracted and combined with clinical characteristics using multivariable linear regression (MLR) to obtain a radiomics-clinical-estimated GFR (rcGFR). The relative contribution of single-kidney rcGFR to overall rcGFR, the percent renal parenchymal volume, and the percent renal hydronephrosis volume were combined by MLR to generate the estimation of SRF (rcphSRF). The Pearson correlation coefficient (r), mean absolute error (MAE), and Lin’s concordance coefficient (CCC) were calculated to evaluate the correlations, differences, and agreements between estimations and SPECT-based measurements, respectively. Results Compared to manual segmentation, deep learning-based automatic segmentation could reduce the average segmentation time by 434.6 times to 3.4 s. Compared to single-kidney GFR measured by SPECT, the rcGFR had a significant correlation of r = 0.75 (p