The aim of this study was to elucidate risk factors associated with postoperative febrile UTI after URS for urinary stones. Data from 153 patients undergoing URS for renal and/or ureteral stones between 2011 and 2013 at a single center were reviewed to detect factors predicting postoperative febrile UTI. URS for residual stones was excluded. Postoperative febrile UTI was defined as body temperature >38 °C and was graded according to the Clavien grading system. The definition of pyuria was 10 or more white blood cells per high power field. Median age of the patients was 57 (range 17–89) years. Of the 153 patients, 98 (64.1 %) were male, 10 (6.5 %) had Eastern Cooperative Oncology Group performance status 2 or greater, 14 (9.2 %) had Charlson comorbidity index 3 or greater. Before URS, 69 (45.1 %) had pyuria, 27 (17.6 %) had acute pyelonephritis, 42 (27.5 %) had ureteral stent, and 50 (32.7 %) were treated with antibiotics. After URS, 28 (18.3 %) developed febrile UTI (Clavien grade I, n = 16; grade II, n = 10; grade III, n = 1; grade IV, n = 1). Preoperative pyuria and acute pyelonephritis were significant factors for postoperative febrile UTI (pyuria: odds ratio 3.62, 95 % CI 1.26–8.11, P value 0.017; pyelonephritis: odds ratio 4.43, 95 % CI 1.06–11.16, P value 0.044). Degree of pyuria was likely to be associated with severity of postoperative febrile UTI, and two cases (1.3 %) with severe pyuria developed sepsis. Careful management is needed for patients with preoperative pyelonephritis or pyuria; risk factors for postoperative febrile UTI to avoid sepsis.