The objective is to compare the prevalence of serious bacterial infection (SBI) and invasive bacterial infection (IBI) in febrile infants <60 days of age and in those between 61 and 90 days. Prospective registry-based cohort study including all the infants ≤90 days with fever without a source evaluated in a pediatric emergency department between 2003 and 2017. We compared the prevalence of SBI and IBI in febrile infants <60 days of age and those between 61 and 90 days. We included 3,301 infants. Overall, 605 (18.3%) had a SBI (mainly urinary tract infection), of these 81 (2.5%) had an IBI (bacteremia 60, meningitis 12, sepsis 9). The prevalence of SBI in infants >60 days old was 18.5% (95% CI: 16.4-20.7) versus 16.6% (95% CI: 14.7-18.7; n.s.) in those between 29 and 60 days and versus 21.5% (95% CI: 18.6-24.7; n.s.) in those <28 days of age. The prevalence of IBI among infants >60 days old was 1.1% (95% CI: 0.6-2.2) versus 2.3% (95% CI: 1.6-3.3; P < 0.05) in those between 29 and 60 days and 5.1% (95% CI: 3.7-7.0; P < 0.05) in those <28 days of age. The prevalence of IBI in well appearing >60 days was 1.0% (versus 4.5% in those <28 days old, P < 0.01; and 2.0% in those between 29 and 60 days, P = 0.06). All bacterial meningitis, except one, were diagnosed in infants <28 days. The prevalence of IBI in febrile infants between 61 and 90 days of age is high enough to support the recommendation for obtaining urine and blood tests in this population.