Background: Timely diagnosis and accurate identification of the causative microorganism in sepsis is crucial in order to offer targeted treatment and increase survival rates. Previous studies have aimed to identify biomarkers that could potentially predict blood culture positivity in patients with bacteremia; however, most of the research has been performed in adult populations. The aims of this study were to analyze procalcitonin (PCT) levels in confirmed bloodstream infections by species in children and assess their utility in immunocompromised patients.Methods: Medical records of children younger than 18 years admitted from 2011 to 2018 were reviewed. Subjects who met the diagnostic criteria for sepsis, with PCT levels collected within a 72-hour period prior to obtaining a blood culture were included. Kruskal-Wallis test was used to compare differences among groups. Receiver-operating characteristic curves were used to evaluate PCT cut-offs. Results: A total of 120 patients were included. Mean age was 55 months. Mean PCT levels in immunosuppressed patients was 26.68 mcg/L, compared to 8.78 in the immunocompetent group. Subjects with bacteremia by Gram-negative bacilli (GNB) had the highest mean PCT levels (18.2 ± 34.2) (p < 0.001). Sensitivity and specificity were 78% and 53% for Gram-positive cocci (GPC), 60.9% and 33.3% for GNB, and 75% and 25% for yeasts, respectively. Subgroup analysis showed 87.5% sensitivity and 16.7% specificity of PCT for predicting documented GNB bacteremia in immunodeficient children. Conclusions: PCT may be considered as a surrogate biomarker in immunocompromised children, and a viable tool to differentiate etiology by species.