Although ureteral stenting is a common conservative treatment for ureteral stricture, it is unclear whether a long-term indwelling ureteral stent protects the kidney against parenchymal atrophy and functional deterioration. In this study, we evaluated the changes in renal parenchymal thickness (RPT) and estimated the glomerular filtration rates (eGFR) in patients with indwelling ureteral stents for one year or more. As a control, we also evaluated changes in RPT associated with indwelling percutaneous nephrostomy (PNS) for one year or more. Polymer ureteral stents were used and replaced every three months. RPT was measured using computed tomography (CT). Totally, 69 renal units in 55 patients with baseline and follow up CT scans available were enrolled. The median follow-up period was 29 months. The etiologies of ureteral obstruction were malignant and benign disease in 27 and 28, respectively. RPT was reduced obviously in most cases. At 1 year, the median reduction rate of RPT was 17.3% in unilateral cases, which was significantly higher than that in the healthy contralateral kidney. There was a strong correlation between eGFR and total RPT including the contralateral kidney. The reduction rate of RPT in kidneys with ureteral stents including bilateral cases was also significantly higher than that in 39 renal units of 35 patients with PNS. The results of this study suggest that the long-term efficacy of indwelling ureteral stents in preserving renal function is limited. Regular imaging may be essential to evaluate the residual renal function.