Background/Objectives: The incidence of late-onset sepsis (LOS) has increased with improved survival rates in premature infants. Blood culture, the diagnostic “gold standard”, requires at least 36–72 h for results, leading to empiric antibiotic use and potential resistance. MicroRNAs (miRNAs) have emerged as promising biomarkers for sepsis in adults, but their role in neonatal LOS remains unclear. The aim of this scoping review is to identify the miRNA expression profiles of bacterial LOS in neonates. Methods: A scoping review of the literature was performed between 1 November 2023 and 31 December 2024. Results: Twelve studies fulfilled our criteria and were included in the review. Despite the considerable heterogeneity among the studies, most focused on detecting and quantifying serum microRNAs using real-time PCR, while some examined correlations with other biomarkers, such as CRP. The few microRNAs identified as common across multiple studies showed similar patterns of regulation in LOS cases. Compared to controls (no LOS), neonates with LOS exhibited significant alterations in miRNA expression. More precisely, in LOS, miRNA-181a, miRNA-23b, miRNA-181b5p, miRNA-21-5p, miRNA-34a5p, miRNA-199a3p, miRNA-1184 and miRNA-1295p were downregulated, while miRNA-16, miRNA-146a, miRNA-101, miRNA-187, miRNA-21, miRNA-15a/16 and miRNA-455-5p were upregulated. Conclusions: Currently, there is limited data regarding miRNA expression in LOS. Many studies showed altered expression of specific miRNAs in septic neonates; however, these observations need further validation in larger cohorts and/or randomized controlled trials to confirm their diagnostic potential.