Abstract Background Early diagnosis and initial therapy are important to reduce the complications of acute bacterial meningitis (ABM). The gold standard in diagnosing bacterial meningitis is by demonstrating the presence of bacteria in cerebrospinal fluid (CSF) samples via CSF cultures. However, CSF culture requires at least a day or more, and has limited sensitivity. Serum procalcitonin (PCT) is one of the most sensitive biomarkers for identification of bacterial from non-bacterial meningitis. This study was done to evaluate serum PCT as a marker to help in ABM diagnosis specially after oral antibiotics intake or when cerebrospinal fluid (CSF) culture is negative and to assess its correlation with outcome of ABM in children. Methods This is a prospective cohort study that included children who presented to Ain Shams University Children hospital over a period of 6 months. Participants were confirmed cases of ABM (laboratory- confirmed by culture) or suspected to have ABM (presented with sudden onset high fever and signs of meningeal irritation with CSF examination showing at least one of the following: 1. turbid appearance; 2. leukocytosis (> 100cells/mm3); 3. leukocytosis (10-100 cells/mm3) and either an a) elevated protein (> 100 mg/dl) or b) decreased glucose (< 40mg/dl)). The PCT levels were measured on admission and 72hours after treatment. Results A total of 38 ABM cases participated in this study. All the 38 cases showed elevated levels of PCT on admission. There was a significant drop in the mean of PCT level after 72h of treatment compared to level on admission (7.1±6.5 vs. 11.4±3.7, p = 0.001) respectively. There was a significant difference in the mean of PCT level between cases with good outcome (full recovery) versus poor outcome (death or neurological sequalae), on admission (7.2±2.8 vs. 13.2±4.4, p < 0.001) and 72h after treatment (4.2±3.5 vs. 12.9±5.3, p < 0.001) respectively. Conclusion Serum PCT levels were high in all patients with ABM, including those who received oral antimicrobials for 1-3 days before admission. The decline in PCT levels after treatment was associated with good outcome in our cohort.