Sepsis has seen an incremental increase in cases of about 13% annually in the USA and accounts for approximately 4400 deaths among pediatric patients. Early identification of the specific pathogen allows the clinician to ensure that the antibiotic coverage is optimal, an intervention that has been shown to improve patient outcomes in sepsis. Our study’s objective was to assess the impact of a rapid Bruker MALDI-Tof identification protocol on pediatric sepsis cases by assessing various indicators. We assessed the quality of care by measuring the following indicators; time to identification of the pathogen, initiation of the most appropriate antibiotic, length of stay (LOS) in hospital and patient outcomes, using a retrospective review over three consecutive years. In total 92 pediatric patients, similar in age and gender distributions were assessed; 37 in 2012, 33 in 2013 and 22 in 2014. The introduction of MALDI-TOF identification in 2013 led to a significant decrease in time to identify a pathogen by 21.03 hours (p = 1.95E-05). A short incubation MALDI-TOF identification protocol in 2014 further reduced time to identification by 17.75 hours (p = 2.48E-3). Overall in 2014 this led to a trend to earlier optimization of antibiotics by 20.2 hours (p = 0.14) and a reduction in length of stay after the implementation of MALDI-ToF identification in 2013 of 3.07 days and a further reduction of 8.92 days after the introduction of the rapid short incubation identification protocol using MALDI-Tof in 2014 (P = 0.12). By evaluating the subgroup of patients where antibiotics were changed, our study confirmed that patients received appropriate therapy 48.8% (20.2 hours) earlier compared to conventional methods leading to a decrease in length of stay of 23.65 days after the implementation of MALDI-ToF identification and a further reduction of 9.82 days in 2014 compared to 2012 (p = 0.02). In 2014 outcomes between the patients needing a change in their antibiotic compared to the patients where the empirical therapy was considered to be optimal were similar with respect to length of stay; 13.04 and 10.93 days (p = 0.34). In the 2012 group there was a significant increase in the length of stay in the group needing change in excess of 30 days (p = 0.02) compared to the group where empirical therapy was considered to be optimal, this clearly showed an improvement in the quality of care received after the rapid identification was instituted in 2014. The 2012 group had a four times overall increased sepsis associated mortality risk compared to the 2014 group and when empirical antibiotics needed to be optimized this risk was 7 times compared to the 2014 group. We conclude that rapid identification of bacterial pathogens in pediatric blood cultures with a rapid incubation MALDI-TOF identification protocol plays an important role in improving quality of care as part of a multidisciplinary approach to pediatric bacteremia and sepsis.