The rise of multidrug-resistant (MDR) infections, which are fuelled by ESKAPE pathogens such as Enterococcus faecium, Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter baumannii, Pseudomonas aeruginosa, and Enterobacter sp., constitutes a severe worldwide health emergency. These bacteria evade antibiotics cleverly by means of genetic mutations, horizontal gene exchange, and the operation of efflux pumps, making many forms of treatment obsolete. To overcome this, we utilize an in silico subtractive genomics approach to identify new drug targets specific to these pathogens. Our target is finding proteins critical for bacterial virulence—but nonvital in humans—to decrease toxicity. Potential target sites include novel bacterial metabolic processes, virulence-related proteins that are essential to infection, and mechanisms that allow resistance. This focused strategy paves the way for safer, more potent antibiotics able to evade the increasing wave of resistance, providing new hope against lethal, drug-resistant infections. Our workflow integrates genome retrieval, clustering of core genes, essentiality analysis, host similarity filtering, pathway annotation, and druggability assessment. For pathogen specificity, we used KEGG-based pathway annotation to limit our attention to functional genes specific to the ESKAPE pathogens. Druggability was subsequently assessed against the Therapeutic Target Database (TTD) via BLASTp, which revealed 31 potential drug targets associated with 60 small molecules. Further molecular docking of the targets against 17 optimized ligands resulted in the identification of four high-affinity protein-ligand complexes. In contrast, rifamycin has broad-spectrum binding ability. This strategy identifies novel drug targets for ESKAPE pathogens and opens the door for next-generation therapeutics against MDR infections.