- We described the occult bacteremia (OB) and bacteremia with diagnosed focus (BwF) picture among children managed as outpatients at the pediatric emergency room (PER) in southern Israel, before and after the introduction of pneumococcal conjugate vaccines (PCVs) introduction in a retrospective study enrolling all three- to 36-month-old patients with fever >38.0 °C during 2005–2014. Of 511 (0.82% of all febrile patients) true bacteremias, 230 (45%) were managed as outpatients; 96 of 230 (41.7%) had OB and 134 (3.59%) had BwF. OB and BwF rates were 0.22% and 3.02%, respectively. A significant decrease was noted in OB and BwF rates (p = 0.0008 and p = 0.02, respectively). S. pneumoniae (SP, 37.5%), K. kingae (11.4%) and Brucella spp. (8.7%) were the most common OB pathogens and SP (29.8%), S. viridans (13.4%), and Brucella spp. (12.7%) were the most common in BwF patients. PCV13 serotypes were not found among the serotypes isolated post-PCV13 introduction. During 2010–2014 there was an increase in non-PCV13 serotype isolation (p = 0.005). SP was the main pathogen isolated among patients with pneumonia, acute otitis media (AOM) and periorbital cellulitis (62.5%, 33.3% and 60%, respectively). OB and BwF decreased following the introduction of PCVs and SP was the main pathogen in both conditions. Vaccine-SP serotypes were not isolated in OB after PCV13 introduction and non-vaccine serotypes increased significantly.