The objective of this prospective observational study was to assess the clinical significance of neutrophil–lymphocyte ratio (NLR), platelet–lymphocyte ratio (PLR) and lymphocyte–monocyte ratio (LMR) as potential biomarkers to identify post-PNL SIRS or sepsis. Demographic data and laboratory data including hemoglobin (Hb), total leucocyte count (TLC), serum creatinine, urine microscopy and culture were collected. The NLR, LMR and PLR were calculated by the mathematical division of their absolute values derived from routine complete blood counts from peripheral blood samples. Stone factors were assessed by non-contrast computerized tomography of kidneys, ureter and bladder (NCCT KUB) and included stone burden (Volume = L × W × D × π × 0.167), location and Hounsfield value and laterality. Intraoperative factors assessed were puncture site, tract size, tract number, operative time, the need for blood transfusion and stone clearance. Of 517 patients evaluated, 56 (10.8%) developed SIRS and 8 (1.5%) developed sepsis. Patients developing SIRS had significantly higher TLC (10.4 ± 3.5 vs 8.6 ± 2.6, OR 1.19, 95% CI 1.09–1.3, p = 0.000002), higher NLR (3.6 ± 2.4 vs 2.5 ± 1.04, OR 1.3, 95% CI = 1.09–1.5, p = 0.0000001), higher PLR (129.3 ± 53.8 vs 115.4 ± 68.9, OR 1.005, 95% CI 1.001–1.008, p = 0.005) and lower LMR (2.5 ± 1.7 vs 3.2 ± 1.8, OR 1.18, 95% CI 1.04–1.34, p = 0.006). Staghorn stones (12.8 vs 3.24%, OR 4.361, 95% CI 1.605–11.846, p = 0.008) and long operative times (59.6 ± 14.01 vs 55.2 ± 16.02, OR 1.01, 95% CI 1.00–1.03, p = 0.05) had significant association with postoperative SIRS. In conclusion, NLR, PLR and LMR can be useful independent, easily accessible and cost-effective predictors for early identification of post-PNL SIRS/sepsis.