Streptococcus agalactiae (Group B Streptococcus; GBS) is the etiological agent of meningitis and severe invasive diseases in newborns. The cellular membrane, a critical site for host-pathogen interactions, is poorly characterized in GBS. Here, we analyzed the GBS lipidome using liquid chromatography coupled with electrospray ionization tandem mass spectrometry. We identified a novel amino-acylated glycolipid, lysyl-glucosyl-diacylglycerol (Lys-Glc-DAG), which is abundant in all GBS strains analyzed. Through heterologous expression and gene deletion, we demonstrate that the GBS multiple peptide resistance factor (MprF) synthesizes Lys-Glc-DAG, as well as lysyl-phosphatidylglycerol (Lys-PG), which has been characterized in many pathogenic bacteria. Consistent with a critical role in host-GBS interactions, the GBSΔmprF mutant exhibited a reduction of surface net negative charge and a significantly reduced ability to invade human cerebral microvascular endothelial cells. Further, mice challenged with the GBSΔmprF mutant developed bacteremia comparably to wild-type GBS-challenged mice, yet exhibited fewer bacterial counts in the brain and less meningeal inflammation. Overall, we demonstrate that GBS has uniquely evolved a multifunctional MprF enzyme that results in the synthesis of a major cationic membrane glycolipid and plays a significant role in meningitis pathogenesis. Moreover, our results illustrate the novel insights obtained from comprehensive lipidomic profiling of major human pathogens.