Ureterorenoscopy (URS) is believed to be a safe and effective procedure to treat ureteral stone or ureteral stricture. Rapidly increased intrarenal pressure during URS may have a negative impact on the kidney, but the effect on renal functions is not well known. The aim of this study is to evaluate whether URS balloon dilation or lithotripsy would cause acute kidney injury (AKI), which was evaluated by urine neutrophil gelatinase associated lipocalin (NGAL) and renal tubular damage, which was evaluated by urine α glutathione S-transferase (GST) and πGST. This prospective study consisted of 207 patients with mean age 53.8 years old between September 2012 and June 2013. Four groups were included: the ureteral stricture group (group 1), the ureteral stone group (group 2), and two control groups. URS induced increased uNGAL on both Days 1 and 14 in both groups, and only elevated u-πGST levels were noted on Day 14 after URSL. On Day 14, the difference between low-grade and high-grade hydronephrosis was significant in group 1 (p < 0.001) rather than group 2 (p = 0.150). By multivariate logistic regression analysis, age, baseline eGFR, and stone size > 1.0 cm were associated with complete recovery of hydronephrosis after URS on Day 14. Ureteral stone patients with preserved renal function suffered more AKI (uNGAL) than those with impaired renal function. However, URS-related AKI had no significant difference between stone ≤ 1 cm and > 1 cm subgroups. Besides, urine αGST and πGST were both significantly higher in stone > 1 cm subgroup when compared to ≤ 1 cm subgroup. In conclusion, URS laser lithotripsy and balloon dilatation all resulted in AKI and renal tubular damage on Day 14 though post-URS double-J (DBJ) stenting was performed in every patient.