BackgroundPresepsin is produced during the phagocytosis of bacteria by granulocytes. Presepsin increases at the site of infection; however, the significance of urinary presepsin in pyelonephritis is unknown. This study aimed to evaluate whether measuring urinary presepsin can distinguish between pyelonephritis and nonpyelonephritis.MethodsA cross-sectional study of patients with suspected pyelonephritis was conducted. Urinary presepsin at admission was compared between the pyelonephritis and nonpyelonephritis groups using the Mann–Whitney test. The predictive accuracy of urinary presepsin for diagnosing pyelonephritis was evaluated by the area under the receiver operating characteristics (ROC) analysis curve.ResultsA total of 35 eligible participants were included in the pyelonephritis group and 25 in the nonpyelonephritis group. The median urinary presepsin level was 2232.0 (interquartile range [IQR], 1029.0–3907.0) pg/mL in the pyelonephritis group and 1348.0 (IQR, 614.5–2304.8) pg/mL in the nonpyelonephritis group. Urinary presepsin concentrations were significantly higher in the pyelonephritis group than in the nonpyelonephritis group (P= 0.023). ROC analysis of urinary presepsin revealed a cutoff value of 3650 pg/mL to distinguish between the pyelonephritis and nonpyelonephritis groups. Sensitivity, specificity, positive predictive value, negative predictive value, positive likelihood ratio, and negative likelihood ratio for the diagnosis of pyelonephritis were 0.40 (95% confidence interval [CI], 0.24–0.58), 0.96 (95% CI, 0.79–1.00), 0.93 (95% CI, 0.68–1.00), 0.52 (95% CI, 0.37–0.68), 9.60 (95% CI, 1.35–68.23), and 0.62 (95% CI, 0.47–0.83), respectively.ConclusionsThe measurement of urinary presepsin is useful in differentiating pyelonephritis from other diseases.Supplementary InformationThe online version contains supplementary material available at 10.1186/s12879-023-08353-2.