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Abstract Background Febrile urinary tract infection (UTI) is common in infants and needs to be diagnosed quickly. However, the symptoms are non-specific, and diagnosis can only be confirmed after high quality urinalysis. The American Academy of Pediatrics recommends suprapubic aspiration (1–9% contamination) and urinary catheterization (8–14% contamination) for urine collection but both these procedures are invasive. Recent studies have shown a new non-invasive method of collecting urine, bladder stimulation, to be quick and safe. However, few data about bacterial contamination rates have been published for this technique. We hypothesize that the contamination rate of urine collection by bladder stimulation to diagnose febrile UTI in infants under 6 months is equivalent to that of urinary catheterization. Methods/design This trial aims to assess equivalence in terms of bacterial contamination of urinary samples collected by urinary catheterization and bladder stimulation to diagnose UTI. Seven hundred seventy infants under 6 months presenting with unexplained fever in one of four Pediatric Emergency Departments in France will be enrolled. Each child will be randomized into a bladder stimulation or urinary catheterization group. The primary endpoints will be the validity of the urine sample assessed by the presence of contamination on bacterial culture. Conclusion A high recruitment rate is achievable due to the high prevalence of suspected UTIs in infants. The medical risk is the same as that for routine clinical care as we analyze patients with isolated fever. If our hypothesis holds true and the rate of urine contamination collected by bladder stimulation is acceptable, the infants included in the study will have benefited from a non-invasive and reliable means of collecting urine. Trial registration ClinicalTrials.gov, NCT03801213. Registered on 11 January 2019.