Salmonellae, gram-negative bacteria, are facultative intracellular pathogens that cause a number of diseases in animals and humans. The poor penetration ability of antimicrobial agents limits their use in the treatment of intracellular bacterial infections. In this study, the cell-penetrating peptides (CPPs) bLFcin6 and Tat11 were separately conjugated to the antimicrobial peptide N2, and the antibacterial activity and pharmacodynamics of the CPPs-N2 conjugates were first evaluated against Salmonellae typhimurium in vitro and in macrophage cells. The cytotoxicity, cellular uptake and mechanism of cellular internalization of the CPPs-N2 conjugates were also examined in RAW264.7 cells. Similar to N2, CPPs-N2 have two reverse β-sheets and three loops. The minimal inhibitory concentration (MIC) of CPPs-N2 was approximately 2 μM, which was higher than that of N2 (0.8 μM). The dose-time curves and cytotoxicity assay showed that both peptide conjugates were more effective than N2 alone at concentrations ranging from 0.25 to 1 × MIC, and they exhibited low cytotoxicity (9.78%-13.54%) at 100 μM. After 0.5 h incubation, the cell internalization ratio of B6N2 and T11N2 exceeded 28.3% and 93.5%, respectively, which was higher than that of N2. The uptake of B6N2 and T11N2 was reduced by low temperature (82.1%-91.7%), chlorpromazine (35.7%-75.1%), and amiloride (26.0%-52.1%), indicating that macropinocytosis and clathrin-mediated endocytosis may be involved. Approximately 98.85% and 91.35% of bacteria were killed within 3 h by T11N2 and B6N2, respectively, which was higher than the percentage killed by N2 (69.74%). Compared with the bactericidal activity of N2 alone, the bactericidal activity of T11N2 and B6N2 was increased by 53.7%-99.6% and 85.3-85.8%, respectively. Both CPPs-N2 conjugates may be excellent candidates for novel antimicrobial agents to treat infectious diseases caused by intracellular pathogens.