Background: Cat scratch disease frequently involves a benign, self-limited disease. Neurological forms associated with Bartonella henselae are uncommon, consisting mostly in neuroretinitis, encephalitis and meningitis. Cerebral epidural empyema has never described. Case presentation: An adult patient was hospitalized for isolated headaches. Magnetic Resonance Imaging (MRI) identified typical features of cerebral epidural empyema. The diagnosis of B. henselae was performed incidentally by 16S rDNA gene sequencing on the abscess fluid, and confirmed by specific qPCR. We report here the first case, to our knowledge, of cerebral epidural empyema associated with B. henselae. Further follow-up visits allowed identifying frequent cat scratches on the scalp as the presumptive source of infection. Conclusions: This case report alerts about such atypical clinical presentation, which requires an extensive clinical investigation. It also emphasizes on the usefulness of additional molecular diagnosis techniques in such CNS infection cases.