The high prevalence of methicillin resistant Staphylococcus aureus (MRSA) and developing resistance to antibiotics requires new approaches for treatment of infectious diseases due to this bacterium. In this study, we developed a targeting agent for selective killing of MRSA using photothermal therapy method based on anti protein A antibody and gold nanorods (GNRs). Polystyrene sulfonate (PSS) coated GNRs were conjugated with anti protein A antibody. The FT-IR and UV-vis analyses approved the formation of anti protein A antibody-gold nanorods conjugate. In vitro study of photothermal therapy showed 82% reduction in the MRSA cells viability which was significantly greater than the ablation effect of free GNRs and laser alone. Significant accumulation of anti protein A antibody-GNRs in the infected muscle in comparison with normal muscle approved the targeting ability of new agent. In vivo study of photothermal therapy resulted in a significant reduction (73%) in the bacterial cells viability in the infected mouse model. These results demonstrated the ability of anti protein A antibody-GNRs conjugate in combination with NIR laser energy for selective killing of MRSA in mouse model.