Bartonella henselae is a fastidious Gram-negative intracellular bacterium which can cause cat scratch disease, endocarditis in humans and animals as well as other complications, leading to acute or chronic infections. The current treatment for Bartonella infections is not very effective due to antibiotic resistance and also persistence. To develop better therapies for persistent and chronic Bartonella infections, in this study, with the help of SYBR Green I/PI viability assay, we performed a high-throughput screening of an essential oil library against stationary phase B. henselae. We successfully identified 32 essential oils that had high activity, including four essential oils extracted from Citrus plants, three from Origanum, three from Cinnamomum, two from Pelargonium and two from Melaleuca, as well as frankincense, ylang ylang, fir needle, mountain savory (winter), citronella, spearmint, elemi, vetiver, clove bud, allspice and cedarwood essential oils. The minimal inhibitory concentration (MIC) determination of these 32 top hits indicated they were not only active against stationary phase non-growing B. henselae but also had good activity against log phase growing B. henselae. The time-kill curve by drug exposure assay showed 13 active hits, including essential oils of oregano, cinnamon bark, mountain savory (winter), cinnamon leaf, geranium, clove bud, allspice, geranium bourbon, ylang ylang, citronella, elemi and vetiver, could eradicate all stationary phase B. henselae cells within 7 days at the concentration of 0.032% (v/v). Two active ingredients, carvacrol and cinnamaldehyde, of oregano and cinnamon bark essential oils, respectively, were shown to be very active against stationary phase B. henselae such that they were able to eradicate all the bacterial cells even at the concentration ≤ 0.01% (v/v). Our finding of active essential oils may help to develop more effective treatments for persistent Bartonella infections.