Objective To study the incidence of postoperative systemic inflammatory response syndrome ( SIRS ) following different antibiotic prophylaxis ( ABP ) regimens in retrograde intrarenal surgery ( RIRS ). Patients and Methods Single‐centre, randomised, controlled trial (August 2014–September 2017) including 426 patients with renal stones with preoperative sterile urine managed by RIRS (ClinicalTrials.gov NCT 02304822). Different ciprofloxacin‐based ABP regimens were used and included a zero dose, single dose (30 min before surgery) or two doses (first dose at 30 min before RIRS and additional dose within 6 h after RIRS). The incidence of SIRS was compared using intention‐to‐treat ( ITT ) and per‐protocol ( PP ) analyses. Results Each group enrolled 142 patients. In the ITT analysis, a zero dose of ABP was statistically similar to the two ABP regimes for the incidence of SIRS (9.9% vs single dose 4.9%, P = 0.112; vs two doses 4.2%, P = 0.062). There were also no relevant differences across groups in the PP analysis; no urosepsis was recorded. In subgroup analysis with stratification by stone area, the three regimens all had a low and similar incidence of SIRS for stones of ≤200 mm 2 in the ITT analysis with a sufficient power value (5.4% vs 6.2% vs 3.6%, P = 0.945 vs single dose and P = 0.553 vs two doses). However, there was a greater chance of SIRS in patients who received no ABP with stones of >200 mm 2 (18% vs single dose 4.3%, P = 0.036; vs two doses 5.5%, P = 0.044). Similar trends were seen in the PP analysis. Conclusions For patients with preoperative sterile urine, ABP is not strongly recommended in patients with stones of ≤200 mm 2 , but for stones >200 mm 2 single‐dose ABP is still required.