A 13-year-old boy with Bartonella henselae meningitis is reported. He presented with recurrent fever with no history of cat scratches and no lymphadenopathy. Cerebrospinal fluid analysis showed an elevated white blood cell count, and Bartonella henselae infection was confirmed by metagenomic next-generation sequencing. Bone marrow examination revealed hemophagocytosis predominantly involving nucleated erythrocytes; to our knowledge, this bone marrow morphological abnormality is the first reported worldwide in association with Bartonella henselae infection. Transient bilateral hip pain occurred during the illness and was considered infection-related joint involvement. The patient improved with treatment and had no neurological sequelae. This case expands the spectrum of clinical and bone marrow manifestations of Bartonella henselae infection and warrants vigilance for possible central nervous system and bone marrow involvement in cases of fever of infectious etiology presenting without typical lymphadenopathy.