Generally Doxycycline, Amoxicillin, Clavulanate-Amoxicillin combination, Enrofloxacin, and Azithromycin are effective.

Regardless of the antibiotic used, a long duration of treatment (4-6 weeks) may be necessary to eliminate infection. Macrolides best represent the oral antibiotic treatments of choice. Fluoroquinolones, alone or in combination with Amoxicillin, have proved fairly effective in dogs. Doxycycline is used in the treatment of certain Bartonella species. However, data from experimentally and naturally infected cats indicates that a high dose (10mg/kg q12h for 4-6 weeks) may also be necessary to eradicate infection of Bartonella henselae in both dogs and cats.