Bacterial multidrug resistance (MDR) is a serious healthcare issue caused by the long-term subtherapeutic clinical treatment of infectious diseases. Nanoscale engineering of metal nanoparticles has great potential to address this issue by tuning the nano-bio interface to target bacteria. Herein, we report the use of branched polyethylenimine-functionalized silver nanoclusters (bPEI-Ag NCs) to selectively kill MDR pathogenic bacteria by combining the antimicrobial activity of silver with the selective toxicity of bPEI toward bacteria. The minimum inhibitory concentration of bPEI-Ag NCs was determined against 12 uropathogenic MDR strains and found to be 10- to 15-fold lower than that of PEI and 2- to 3-fold lower than that of AgNO3 alone. Cell viability and hemolysis assays demonstrated the biocompatibility of bPEI-Ag NCs with human fibroblasts and red blood cells, with selective toxicity against MDR bacteria.