Neoehrlichiosis caused by N. mikurensis is a rare infection in humans, however it is gaining increased attention as an emerging tick-borne zoonosis in immunocompromised patients in Europe. Here we report on the first case of human neoehrlichiosis in Germany, which occurred in a 66-year-old woman with a history of granulomatosis with polyangiitis (GPA), B-cell depletion therapy, and secondary antiphospholipid syndrome. While undergoing long-term treatment for GPA with the anti-CD20 antibody rituximab, the patient was hospitalized because of a prolonged fever of unknown origin (FUO) and hyperinflammatory syndrome. Neoehrlichiosis was diagnosed directly through eubacterial 16S rDNA PCR screening of EDTA whole blood from the patient. This was followed by a genetic sequence analysis of the amplicon. The patient was treated with doxycycline whereby her condition eventually improved and the parasite was cleared. Our findings suggest that human neoehrlichiosis can occur in Germany and that, in areas of endemicity, N. mikurensis should be taken into consideration in immunocompromised individuals with FUO and signs of infection.