Introduction: Urinary tract infection (UTI) is the leading cause of bacterial infection in infants younger than 3 months of age with fever without a source. Objective: The objective of the study was to analyze the characteristics of emergency department presentations of febrile infants younger than 3 months of age with a UTI and identify risk factors for invasive bacterial infection (IBI) secondary to UTI. Methods: This was a secondary analysis of a prospective observational registry that includes infants younger than 3 months with fever without a source managed at a pediatric emergency department between 2003 and 2019. Results: Of the 2850 patients included, 592 (20.8%) were diagnosed with a UTI (524, 88.5%, for Escherichia coli). Infants with UTIs showed significant clinical differences when compared with those not diagnosed with a bacterial infection: patients with a UTI were more likely to have a history of renal/urological problems (8.3% vs. 3.5%), temperature ≥39ºC (38.3% vs. 29%) and poor feeding (13% vs. 8.7%). Yet, nearly half (285 of the 592, 48.1%) of the infants with febrile UTIs had none of these 3 risk factors. Thirty-six infants (6.1%) had a secondary IBI. We identified the following independent risk factors for secondary IBI: infants younger than 1 month of age, parent-reported irritability, procalcitonin >0.5 ng/mL, and C-reactive protein >60 mg/L. Conclusions: History and physical examination do not allow us to safely rule out a UTI among young febrile infants. Age, parent-reported irritability, and biomarkers are useful in identifying patients at increased risk of secondary IBI.