Myriad operative factors and characteristics of patients may influence the risk of infection in a patient undergoing stone surgery. We prospectively determined the risk factors for systemic inflammatory response syndrome (SIRS) and quick sequential organ failure assessment (qSOFA) in patients undergoing percutaneous nephrolithotomy (PCNL) and retrograde intrarenal surgery (RIRS). Patients who underwent PCNL and RIRS from March 2018 to January 2020 satisfying our selection criteria were enrolled. Samples of urine from the renal pelvis, bladder, and retrieved stones were sent for culture testing. Postoperatively patients were keenly supervised for any indications of SIRS and qSOFA. The association between stone and urine cultures across various sites was examined. Regression analysis was performed to ascertain clinical variables affiliated with SIRS and qSOFA. The study included a total of 150 patients including both PCNL and RIRS, of which 23% post-PCNL and 20% post-RIRS met the criteria of SIRS and qSOFA. On univariate analysis in PCNL-Dilated pelvicalyceal system (PCS), renal pelvic urine culture (RPUC), stone culture (SC), and operative time >124 min among others were identified as risk factors whereas, in RIRS-residual calculus, RPUC, SC and operative time >62 min were risk factors. Multivariate analysis identified dilated PCS and SC for PCNL and only intraoperative RPUC for RIRS as independent risk factors. Only a significantly strong correlation among culture analysis was found between RPUC and SC in both the procedures. Intraoperative RPUC and SCs are better predictors of post-PCNL SIRS while Intraoperative RPUC and duration of surgery are better predictors of post-RIRS sepsis. We, therefore, recommend that both these cultures must routinely be obtained in the above procedures to identify the offending organisms and amend antibiotic therapy during treatment and surgical duration should be kept <62 min in RIRS. SIRS serves as a sensitive review tool which is specifically useful for initial care and on the contrary qSOFA is well suited for patients at greater risk of demise, thereby guiding clinicians to decide future care and course of treatment of patients.