The efficiency of simultaneous treatment of the cold atmospheric pressure plasma jet (CAP) and hydrogen peroxide (H2O2) was investigated. A CAP with a thin and long plume was generated with Ar gas and applied to a common oral bacterium, Enterococcus faecalis (E. faecalis). The bactericidal efficiency was evaluated with the electron microscopy and the colony forming unit (CFU) assay. The underlying mechanisms were studied by measuring extracellular chemical changes in the water solution and by measuring biological responses such as the trans-membrane potential, the intracellular oxidative stress, and the membrane permeability. The combination of CAP with H2O2 could provide dramatic synergistic effects in bacterial disinfection through the enhanced membrane transportation of reactive species and the oxidation of intracellular molecules. Since the byproducts of both H2O2 and CAP are not significantly toxic, the synergistic bactericidal effects of their combination could be a good candidate to clinical applications.