Ureterorenoscopy (URS) is believed to be a safe and effective procedure for treating ureteral stones or ureteral strictures. Rapidly increasing intrarenal pressure during URS may have a negative impact on the kidney, but its effect on renal function is not well known. The aim of this study was to evaluate whether URS balloon dilation or lithotripsy could cause acute kidney injury (AKI), which was evaluated using urine neutrophil gelatinase-associated lipocalin (NGAL), and renal tubular damage, which was evaluated using urine α-glutathione S-transferase (GST) and πGST. This prospective study included 207 patients with a mean age of 53.8 years 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 increased urine NGAL (uNGAL) levels on days 1 and 14 in both groups, and only elevated uGST levels were noted on day 14 after URS lithotripsy (URS). On day 14, the difference between low-grade and high-grade hydronephrosis was significant in group 1 (
p
<
0.001
) compared to that in group 2 (
p
=
0.150
). Multivariate logistic regression analysis revealed that age, baseline estimated glomerular filtration rate (eGFR), and
stone
size
>
1.0
cm were associated with the complete recovery of hydronephrosis after URS on day 14. Patients with ureteral stones with preserved renal function had more AKI than those with impaired renal function. However, there was no significant difference in URS-related AKI between the ≤1 cm and >1 cm subgroups. In addition, urine αGST and πGST levels were both significantly higher in the
stone
>
1
cm subgroup than in the ≤1 cm subgroup. In conclusion, URS laser lithotripsy and balloon dilatation resulted in AKI and renal tubular damage on day 14, although post-URS double-J (DBJ) stenting was performed in every patient.