Autoimmune neutropenia of infancy is characterized by recurrent infections such as pneumonia, otitis media, impetigo, purulent skin regions, gastritis, and upper respiratory infection. However, severe bacterial infection is uncommon. This report documents a 9-month-old boy presenting with autoimmune neutropenia in association with multiple brain abscesses during the course of human herpesvirus (HHV)-6 infection. HHV-6 has a tendency of neurovirulence, which can destroy the blood-brain barrier and facilitate the easy invasion of agents inside the brain. Although autoimmune neutropenia of infancy is benign and self limiting, it must be emphasized that severe bacterial infection will be induced by concurrent viral infection in this specific disorder.