It’s urgently needed to find new repurposed antibacterial drugs as the desired novel choices to counter biofilms and persister of gram-positive bacteria. Several reports have supported that Fingolimod, which was approved by FDA as a novel drug for the treatment of relapsing multiple sclerosis, can kill the bacteria by selectively disrupting the cell membrane of bacteria. However, the action mode and mechanism of Fingolimod against gram-positive bacteria remains elusive. Our data indicated that Fingolimod exerted the bactericidal activity against a wide spectrum of gram-positive bacteria, including Staphylococcus aureus, Enterococcus faecalis, Streptococcus agalactiae et al. Moreover, Fingolimod could significantly eliminate the persister, inhibit biofilm formation, eradicate mature biofilm in vitro against S. aureus. Fingolimod rapidly eradicated S. aureus by pH-dependent disruption of the bacterial cell membrane's permeability and integrity, with its minimum inhibitory concentration (MIC) increasing up to 16-fold in response to elevated concentrations of phospholipids CL, PG, and PE. After four months of Fingolimod exposure, the MIC values of S. aureus showed a slight increase, and three genetic mutations related to phospholipid metabolism—PhoP, AcpP, and PhoU2—were identified in Fingolimod-induced clones, suggesting that Fingolimod may disrupt the cell membrane by targeting phospholipids. Overall, Fingolimod kills S. aureus by disrupting the bacteria membrane and targeting the phospholipids within the cell membrane. This study first reveals that Fingolimod kills S. aureus by targeting cell membrane phospholipids, a mechanism similar to cationic bactericides.